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######## Download mature miRNA data #######
gdcRNADownload(project.id = 'TARGET-NBL',

•             data.type      = 'miRNAs',
  

•             write.manifest = FALSE,
  

•             method         = 'gdc-client',
  

•             directory      = mirdir)
  

incomplete final line found by readTableHeader on 'https://api.gdc.cancer.gov/files?filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TARGET-NBL%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%22Transcriptome%20Profiling%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:%22Isoform%20Expression%20Quantification%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:%22BCGSC%20miRNA%20Profiling%22%7D%7D]%7D&pretty=true&format=JSON&size=10000&expand=analysis,analysis.input_files,associated_entities,cases,cases.diagnoses,cases.diagnoses.treatments,cases.demographic,cases.project,cases.samples,cases.samples.portions,cases.samples.portions.analytes,cases.samples.portions.analytes.aliquots,cases.samples.portions.slides&return_type=manifest'Successfully downloaded: 0

I was trying to follow the instruction by running the step of paring metadata of RNA files of TCGA-CHOL project. And it returned no output. However, the query of miRNAs one worked.

> metaMatrix.RNA <- gdcParseMetadata(project.id = 'TCGA-CHOL',
                                   data.type  = 'RNAseq', 
                                   write.meta = FALSE)
> metaMatrix.RNA
 [1] file_name              file_id                patient               
 [4] sample                 submitter_id           entity_submitter_id   
 [7] sample_type            gender                 age_at_diagnosis      
[10] tumor_stage            tumor_grade            days_to_death         
[13] days_to_last_follow_up vital_status           project_id            
<0 rows> (or 0-length row.names)

Can you please look into this issue? Thanks!

gdcParseMetadata error

> metaMatrix.RNA <- gdcParseMetadata(metafile = "./metadata.cart.2020-05-08.json")
Error in vapply(seq_len(nSam), function(i) metadata[[i]]$cases[[1]]$samples[[1]]$submitter_id,  : 
  值的长度必需为1，
 但FUN(X[[1]])结果的长度却是0

The metadata.cart.2020-05-08.json file head is

[{
  "file_id": "ccf08842-c001-43be-b2c4-7a37499dcd18", 
  "associated_entities": [
    {
      "entity_submitter_id": "TCGA-71-6725-01A-11R-1858-07", 
      "entity_id": "9680a78d-59ab-4cf0-bd92-e6ecbc640e04", 
      "entity_type": "aliquot", 
      "case_id": "4b7cd595-e7f9-45a8-b736-a8c7c42d9539"
    }
  ], 
  "state": "released", 
  "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
  "file_name": "5d420937-4d97-4f04-9ce9-754054261d97.htseq.counts.gz", 
  "experimental_strategy": "RNA-Seq", 
  "access": "open", 
  "data_format": "TXT", 
  "data_type": "Gene Expression Quantification", 
  "data_category": "Transcriptome Profiling", 
  "analysis": {
    "analysis_id": "390fff89-0e17-41c2-b0c5-2de8124271f0", 
    "input_files": [
      {
        "file_id": "745f6641-f01a-4c42-9883-f36872514020", 
        "state": "released", 
        "updated_datetime": "2018-11-15T21:12:37.513272-06:00", 
        "data_category": "Sequencing Reads", 
        "created_datetime": "2016-05-27T22:03:53.926564-05:00", 
        "file_name": "792a9dd3-28b5-42f5-aa23-e64f47995f9a_gdc_realn_rehead.bam", 
        "experimental_strategy": "RNA-Seq", 
        "access": "controlled", 
        "data_format": "BAM", 
        "data_type": "Aligned Reads", 
        "submitter_id": "792a9dd3-28b5-42f5-aa23-e64f47995f9a", 
        "md5sum": "d95c94ce0b5f02e70c6e7df27dc7d478", 
        "file_size": 10602206295, 
        "platform": "Illumina"
      }
    ], 
    "workflow_link": "https://github.com/NCI-GDC/htseq-cwl", 
    "updated_datetime": "2018-09-06T21:10:41.393019-05:00", 
    "submitter_id": "5d420937-4d97-4f04-9ce9-754054261d97_count", 
    "created_datetime": "2016-05-29T10:24:46.178710-05:00", 
    "state": "released", 
    "workflow_version": "v1", 
    "workflow_type": "HTSeq - Counts"
  }, 
  "md5sum": "f8b64783717da58198a723cfa52f0723", 
  "file_size": 254695
}

Hi,

I was using GDCRNATools to perform 'Functional enrichment analysis'. Here is the command that I used: enrichOutput <- gdcEnrichAnalysis(gene = rownames(deALL), simplify = TRUE).But the following error popped up. I have checked instructions of gdcEnrichAnalysis command, but I did not get how to setup species in gdcEnrichAnalysis(). Can you check for me please? Thank you in advance!

### This step may take a few minutes ###

Step 1/5: BP analysis done!
Step 2/5: CC analysis done!
Step 3/5: MF analysis done!
Error in download.KEGG.Path(species) : 
  'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...

Best,

Jianxiang

I'm trying to use 'gdcParseMetadata()' to parse metadata by providing the metadata file, but find that the format of the metadata file in GDC has been change recently.
So, I want to know how long the GDCRNATools can be updated.
Thanks!

`
##############################################################################

Error in vapply(seq_len(nSam), function(i) metadata[[i]]$cases[[1]]$samples[[1]]$submitter_id, :
值的长度必需为1，
但FUN(X[[1]])结果的长度却是0
Calls: source ... withVisible -> eval -> eval -> gdcParseMetadata -> vapply
停止执行
`

I installed R-3.4.1 by Miniconda, and managed to installed the GDCRNATools, but while testing with your instruction to download RNA data (http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html#data-preparation), I got a error when using gdcRNADownload(). The error is like this:

and my sessionInfo() is below:

Do you have any idea why I got this problem and how to solve? Thank you so much!

Hi all!!

I've been trying to use the function gdcRNADownload() to download RNAseq data from TCGA but no matter what RNAseq type I try, I always get the same error:

Successfully downloaded: 0
Warning message:
In read.table(paste(url, "&return_type=manifest", sep = ""), header = TRUE, :
incomplete final line found by readTableHeader on 'https://api.gdc.cancer.gov/files?filters=%7B%22op%22:%22and%22,%22content%22:[%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22cases.project.project_id%22,%22value%22:[%22TCGA-CHOL%22]%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_category%22,%22value%22:%22Transcriptome%20Profiling%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.data_type%22,%22value%22:%22Gene%20Expression%20Quantification%22%7D%7D,%7B%22op%22:%22in%22,%22content%22:%7B%22field%22:%22files.analysis.workflow_type%22,%22value%22:%22HTSeq%20-%20Counts%22%7D%7D]%7D&pretty=true&format=JSON&size=10000&expand=analysis,analysis.input_files,associated_entities,cases,cases.diagnoses,cases.diagnoses.treatments,cases.demographic,cases.project,cases.samples,cases.samples.portions,cases.samples.portions.analytes,cases.samples.portions.analytes.aliquots,cases.samples.portions.slides&return_type=manifest'

It only happens with RNAseq type of data. I can download miRNAs data without problems. Initially I was working on a Macbook air with M1 chip:

sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages:
[1] stringr_1.4.0 readxl_1.4.0 tibble_3.1.6 oligo_1.56.0
[5] Biostrings_2.60.2 GenomeInfoDb_1.28.4 XVector_0.32.0 IRanges_2.26.0
[9] S4Vectors_0.30.2 oligoClasses_1.54.0 GEOquery_2.60.0 Biobase_2.52.0
[13] BiocGenerics_0.38.0 edgeR_3.34.1 limma_3.48.3 GDCRNATools_1.13.1

loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.1.2 RSQLite_2.2.12
[4] AnnotationDbi_1.54.1 htmlwidgets_1.5.4 grid_4.1.1
[7] BiocParallel_1.26.2 scatterpie_0.1.7 munsell_0.5.0
[10] codetools_0.2-18 preprocessCore_1.54.0 DT_0.22
[13] colorspace_2.0-3 GOSemSim_2.18.1 filelock_1.0.2
[16] knitr_1.38 rstudioapi_0.13 ggsignif_0.6.3
[19] DOSE_3.18.3 pathview_1.32.0 MatrixGenerics_1.4.3
[22] KEGGgraph_1.52.0 GenomeInfoDbData_1.2.6 KMsurv_0.1-5
[25] polyclip_1.10-0 bit64_4.0.5 farver_2.1.0
[28] downloader_0.4 vctrs_0.4.0 treeio_1.16.2
[31] generics_0.1.2 xfun_0.30 BiocFileCache_2.0.0
[34] affxparser_1.64.1 R6_2.5.1 graphlayouts_0.8.0
[37] locfit_1.5-9.5 bitops_1.0-7 cachem_1.0.6
[40] fgsea_1.18.0 gridGraphics_0.5-1 DelayedArray_0.18.0
[43] assertthat_0.2.1 promises_1.2.0.1 scales_1.1.1
[46] ggraph_2.0.5 enrichplot_1.12.3 gtable_0.3.0
[49] tidygraph_1.2.1 rlang_1.0.2 genefilter_1.74.1
[52] splines_4.1.1 rstatix_0.7.0 lazyeval_0.2.2
[55] broom_0.7.12 BiocManager_1.30.16 reshape2_1.4.4
[58] abind_1.4-5 backports_1.4.1 httpuv_1.6.5
[61] qvalue_2.24.0 clusterProfiler_4.0.5 tools_4.1.1
[64] ggplotify_0.1.0 ggplot2_3.3.5 affyio_1.62.0
[67] ellipsis_0.3.2 gplots_3.1.1 ff_4.0.5
[70] RColorBrewer_1.1-3 Rcpp_1.0.8.3 plyr_1.8.7
[73] progress_1.2.2 zlibbioc_1.38.0 purrr_0.3.4
[76] RCurl_1.98-1.6 prettyunits_1.1.1 ggpubr_0.4.0
[79] viridis_0.6.2 cowplot_1.1.1 zoo_1.8-9
[82] SummarizedExperiment_1.22.0 ggrepel_0.9.1 magrittr_2.0.3
[85] data.table_1.14.2 DO.db_2.9 survminer_0.4.9
[88] matrixStats_0.61.0 hms_1.1.1 patchwork_1.1.1
[91] mime_0.12 xtable_1.8-4 XML_3.99-0.9
[94] gridExtra_2.3 compiler_4.1.1 biomaRt_2.48.3
[97] KernSmooth_2.23-20 crayon_1.5.1 shadowtext_0.1.1
[100] htmltools_0.5.2 ggfun_0.0.6 later_1.3.0
[103] tzdb_0.3.0 tidyr_1.2.0 geneplotter_1.70.0
[106] aplot_0.1.3 DBI_1.1.2 tweenr_1.0.2
[109] dbplyr_2.1.1 MASS_7.3-56 rappdirs_0.3.3
[112] Matrix_1.4-1 car_3.0-12 readr_2.1.2
[115] cli_3.2.0 igraph_1.3.0 km.ci_0.5-2
[118] GenomicRanges_1.44.0 pkgconfig_2.0.3 xml2_1.3.3
[121] foreach_1.5.2 ggtree_3.0.4 annotate_1.70.0
[124] yulab.utils_0.0.4 digest_0.6.29 graph_1.70.0
[127] cellranger_1.1.0 fastmatch_1.1-3 survMisc_0.5.5
[130] tidytree_0.3.9 curl_4.3.2 shiny_1.7.1
[133] gtools_3.9.2 rjson_0.2.21 lifecycle_1.0.1
[136] nlme_3.1-157 GenomicDataCommons_1.16.0 jsonlite_1.8.0
[139] carData_3.0-5 viridisLite_0.4.0 fansi_1.0.3
[142] pillar_1.7.0 lattice_0.20-45 KEGGREST_1.32.0
[145] fastmap_1.1.0 httr_1.4.2 survival_3.3-1
[148] GO.db_3.13.0 glue_1.6.2 png_0.1-7
[151] iterators_1.0.14 bit_4.0.4 Rgraphviz_2.36.0
[154] ggforce_0.3.3 stringi_1.7.6 blob_1.2.2
[157] DESeq2_1.32.0 org.Hs.eg.db_3.13.0 caTools_1.18.2
[160] memoise_2.0.1 dplyr_1.0.8 ape_5.6-2

But I also have the same issue when I try to execute the same function in the cluster:

sessionInfo()

R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Springdale Linux 7.9 (Verona)

Matrix products: default
BLAS/LAPACK: /ifs/data/fg2532_lab/jc5737/Conda_env/lib/libopenblasp-r0.3.18.so

locale:
[1] C

attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base

other attached packages:
[1] stringr_1.4.0 readxl_1.4.0 tibble_3.1.6
[4] oligo_1.58.0 Biostrings_2.62.0 GenomeInfoDb_1.30.1
[7] XVector_0.34.0 IRanges_2.28.0 S4Vectors_0.32.4
[10] oligoClasses_1.56.0 GEOquery_2.62.2 Biobase_2.54.0
[13] BiocGenerics_0.40.0 edgeR_3.36.0 limma_3.50.1
[16] GDCRNATools_1.14.0

loaded via a namespace (and not attached):
[1] utf8_1.2.2 tidyselect_1.1.2
[3] RSQLite_2.2.12 AnnotationDbi_1.56.2
[5] htmlwidgets_1.5.4 grid_4.1.3
[7] BiocParallel_1.28.3 scatterpie_0.1.7
[9] munsell_0.5.0 preprocessCore_1.56.0
[11] codetools_0.2-18 DT_0.22
[13] colorspace_2.0-3 GOSemSim_2.20.0
[15] filelock_1.0.2 knitr_1.38
[17] ggsignif_0.6.3 DOSE_3.20.1
[19] pathview_1.34.0 MatrixGenerics_1.6.0
[21] KEGGgraph_1.54.0 GenomeInfoDbData_1.2.7
[23] KMsurv_0.1-5 polyclip_1.10-0
[25] bit64_4.0.5 farver_2.1.0
[27] downloader_0.4 vctrs_0.4.0
[29] treeio_1.18.1 generics_0.1.2
[31] xfun_0.30 BiocFileCache_2.2.1
[33] affxparser_1.66.0 R6_2.5.1
[35] graphlayouts_0.8.0 locfit_1.5-9.5
[37] bitops_1.0-7 cachem_1.0.6
[39] fgsea_1.20.0 gridGraphics_0.5-1
[41] DelayedArray_0.20.0 assertthat_0.2.1
[43] promises_1.2.0.1 scales_1.1.1
[45] ggraph_2.0.5 enrichplot_1.14.2
[47] gtable_0.3.0 tidygraph_1.2.1
[49] rlang_1.0.2 genefilter_1.76.0
[51] splines_4.1.3 rstatix_0.7.0
[53] lazyeval_0.2.2 broom_0.7.12
[55] BiocManager_1.30.16 reshape2_1.4.4
[57] abind_1.4-5 backports_1.4.1
[59] httpuv_1.6.5 qvalue_2.26.0
[61] clusterProfiler_4.2.2 tools_4.1.3
[63] ggplotify_0.1.0 ggplot2_3.3.5
[65] affyio_1.64.0 ellipsis_0.3.2
[67] gplots_3.1.1 ff_4.0.5
[69] RColorBrewer_1.1-3 Rcpp_1.0.8.3
[71] plyr_1.8.7 progress_1.2.2
[73] zlibbioc_1.40.0 purrr_0.3.4
[75] RCurl_1.98-1.6 prettyunits_1.1.1
[77] ggpubr_0.4.0 viridis_0.6.2
[79] zoo_1.8-9 SummarizedExperiment_1.24.0
[81] ggrepel_0.9.1 magrittr_2.0.3
[83] data.table_1.14.2 DO.db_2.9
[85] survminer_0.4.9 matrixStats_0.61.0
[87] hms_1.1.1 patchwork_1.1.1
[89] mime_0.12 xtable_1.8-4
[91] XML_3.99-0.9 gridExtra_2.3
[93] compiler_4.1.3 biomaRt_2.50.3
[95] KernSmooth_2.23-20 crayon_1.5.1
[97] shadowtext_0.1.1 htmltools_0.5.2
[99] ggfun_0.0.6 later_1.3.0
[101] tzdb_0.3.0 tidyr_1.2.0
[103] geneplotter_1.72.0 aplot_0.1.3
[105] DBI_1.1.2 tweenr_1.0.2
[107] dbplyr_2.1.1 MASS_7.3-56
[109] rappdirs_0.3.3 Matrix_1.4-1
[111] car_3.0-12 readr_2.1.2
[113] cli_3.2.0 parallel_4.1.3
[115] igraph_1.3.0 GenomicRanges_1.46.1
[117] pkgconfig_2.0.3 km.ci_0.5-6
[119] xml2_1.3.3 foreach_1.5.2
[121] ggtree_3.2.1 annotate_1.72.0
[123] yulab.utils_0.0.4 digest_0.6.29
[125] graph_1.72.0 cellranger_1.1.0
[127] fastmatch_1.1-3 survMisc_0.5.6
[129] tidytree_0.3.9 curl_4.3.2
[131] shiny_1.7.1 gtools_3.9.2
[133] rjson_0.2.21 lifecycle_1.0.1
[135] nlme_3.1-157 GenomicDataCommons_1.18.0
[137] jsonlite_1.8.0 carData_3.0-5
[139] viridisLite_0.4.0 fansi_1.0.3
[141] pillar_1.7.0 lattice_0.20-45
[143] KEGGREST_1.34.0 fastmap_1.1.0
[145] httr_1.4.2 survival_3.3-1
[147] GO.db_3.14.0 glue_1.6.2
[149] png_0.1-7 iterators_1.0.14
[151] bit_4.0.4 Rgraphviz_2.38.0
[153] ggforce_0.3.3 stringi_1.7.6
[155] blob_1.2.2 DESeq2_1.34.0
[157] org.Hs.eg.db_3.14.0 caTools_1.18.2
[159] memoise_2.0.1 dplyr_1.0.8
[161] ape_5.6-2

So I don't know how to solve the problem because when I try to troubleshoot the gdcRNADownload() function and follow line by line the code, it says that one of the inner functions (gdcGetURL()) it's not found. So I don't know where the error comes from because I can't access the URL containing the RNAseq data. It might even be a format problem with the downloaded data. I know this issue was reported before but given there was no follow-through, I thought a new threat might bring a bit more attention. Sorry guys and thanks a lot for your help!

Josu

Hello!

my name is Natasha and I am following the tutorial on http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html#cernas-network-analysis-of-degs

I have 273 miRNAs and mRNAs on my expression table. However, when I give the following command:

ceOutput <- gdcCEAnalysis(lnc = rownames(deLNC),
pc = rownames(dePC),
lnc.targets = 'starBase',
pc.targets = 'starBase',
rna.expr = mrna2,
mir.expr = mirna2)

It gives me this error:

Step 1/3: Hypergenometric test done !
Error in cor.test.default(lncDa, mirDa, alternative = "less") :
not enough finite observations

there are 99 deLNC and 1622 dePC (FDR <= 0.05)

Please, can you help me? Where did I do wrong?

best wishes,
Natasha

When I try to run the following code taken from the help passage of gdcCorPlot,

genes <- c('ENSG00000000938','ENSG00000000971','ENSG00000001036',
           'ENSG00000001084','ENSG00000001167','ENSG00000001460')

samples <- c('TCGA-2F-A9KO-01', 'TCGA-2F-A9KP-01', 
             'TCGA-2F-A9KQ-01', 'TCGA-2F-A9KR-11', 
             'TCGA-2F-A9KT-11', 'TCGA-2F-A9KW-11')

metaMatrix <- data.frame(sample_type=rep(c('PrimaryTumor',
                                           'SolidTissueNormal'),each=3),
                         sample=samples,
                         days_to_death=seq(100,600,100),
                         days_to_last_follow_up=rep(NA,6))

rnaExpr <- matrix(c(2.7,7.0,4.9,6.9,4.6,2.5,
                    0.5,2.5,5.7,6.5,4.9,3.8,
                    2.1,2.9,5.9,5.7,4.5,3.5,
                    2.7,5.9,4.5,5.8,5.2,3.0,
                    2.5,2.2,5.3,4.4,4.4,2.9,
                    2.4,3.8,6.2,3.8,3.8,4.2),6,6)
rownames(rnaExpr) <- genes
colnames(rnaExpr) <- samples
gdcCorPlot(gene1 = 'ENSG00000000938', 
           gene2    = 'ENSG00000001084',
           rna.expr = rnaExpr,
           metadata = metaMatrix)

I get the following error message

`geom_smooth()` using formula 'y ~ x'
Warning messages:
1: Use of `corDa$lncDa` is discouraged. Use `lncDa` instead. 
2: Use of `corDa$pcDa` is discouraged. Use `pcDa` instead. 
3: Use of `corDa$lncDa` is discouraged. Use `lncDa` instead. 
4: Use of `corDa$pcDa` is discouraged. Use `pcDa` instead. 
5: Removed 3 rows containing missing values (geom_point). 

and the output is as follows, which seem to have remove all three samples corresponding to SolidTissueNormal.

用gdcCEAnalysis的时候，lnc.target设‘spongeScan’会报错，设为‘starBase’和‘miRcode’想去甚远。starBase最后的node在33左右，而用miRcode会有700+ node。而且设定了deMIR，运算出来的结果还是包含了非deMIR里的数据

I download clinical data fellowed the GDCRNATools Manual
I got a error when using gdcClinicalMerge(). The error is like this:

> clinicalDa <- gdcClinicalMerge(path = clinicaldir, key.info = TRUE)
############### Merging Clinical data ###############

Error in apply(t3, 2, function(v) max(as.numeric(v))) : 
  dim(X) must have a positive length

When using the follwing code:

####### Download mature miRNA data #######
gdcRNADownload(project.id     = 'TCGA-BRCA', 
               data.type      = 'miRNAs', 
               write.manifest = FALSE,
               method         = 'gdc-client',
               directory      = mirdir)

• I got the following error, that haven't been solved.*

ERROR: An unexpected error has occurred during normal operation of the client. Please report the following exception to GDC support [email protected].
ERROR: 'NoneType' object has no attribute 'status_code'
Traceback (most recent call last):
File "gdc-client", line 99, in
File "build\bdist.win-amd64\egg\gdc_client\download\parser.py", line 111, in download
File "build\bdist.win-amd64\egg\gdc_client\download\client.py", line 234, in download_small_groups
File "build\bdist.win-amd64\egg\gdc_client\download\client.py", line 171, in download_tarfile
AttributeError: 'NoneType' object has no attribute 'status_code'
ERROR: Exiting
Traceback (most recent call last):
File "logging_init.py", line 861, in emit
File "logging_init_.py", line 734, in format
File "build\bdist.win-amd64\egg\gdc_client\log\log.py", line 36, in format
File "logging_init_.py", line 465, in format
File "logging_init_.py", line 325, in getMessage
TypeError: str returned non-string (type SysCallError)
Logged from file client.py, line 150

Hello

I try to test GDCRNATools with the same project (TCGA-CHOL), I have this error in gdcRNAMerge :

Error in gzfile(filenames[1]) : invalid 'description' argument

Someone has solved this error ?

When I use it to build ceRNA network,I notice the internal dataset "pcTarget" and "lncTarget" of this package.

QUESTION:
According to your published article,you use 3 data sources including StarBase v2.0 (Li et al.,2014), miRcode (Jeggari et al., 2012), and spongeScan (Furio´ -Tarı´et al., 2016).So I was confused when I found only 137 lncRNAs in lncTarget dataset.Whether you use intersect or union of them?
Because starBase had been updated to v3.0 with 531 lncRNAs with miRNA interaction.I wonder whether to use my new data.Counld you give some suggestion?

ADVICE:
I found an error would appear if some miRNAs in the matrix of users didn't exist in the "pcTarget"/ "lncTarget" or self-defined datasets of users.And I think the next code for mirCorTestFun function would avoid this problems.Your suggestion?

mirCorTestFun <- function(lncDa,pcDa, mir,mir.expr) { if(mir %in% rownames(mir.expr)){ ## miRNA in the matrix(your raw codes) mirDa <- unlist(mir.expr[mir,]) corlm <- cor.test(lncDa, mirDa, alternative='less') corpm <- cor.test(pcDa, mirDa, alternative='less') reglm <- corlm$estimate regpm <- corpm$estimate } else { ## miRNA not exist,so correlation could not be calculated. reglm <- NA regpm <- NA } return (c(reglm, regpm)) ## lnc then pc }

Look forward to your return.Thank you!

When I try the following code

library(GDCRNATools)
library(limma)
data(lncTarget)
data("pcTarget")
data("DEGAll")
data("mirCounts")
data("rnaCounts")

Normalization of RNAseq data

rnaExpr <- gdcVoomNormalization(counts = rnaCounts, filter = FALSE)
####### Normalization of miRNAs data #######
mirExpr <- gdcVoomNormalization(counts = mirCounts, filter = FALSE)

deLNC <- gdcDEReport(deg = DEGAll, gene.type = 'long_non_coding')
dePC <- gdcDEReport(deg = DEGAll, gene.type = 'protein_coding')
ceOutput <- gdcCEAnalysis(lnc = rownames(deLNC), pc = rownames(dePC), lnc.targets = lncTarget, pc.targets = pcTarget, rna.expr = rnaExpr, mir.expr = mirExpr)

I get this error: Error in rna.expr[pc, ] : subscript out of bounds

I am trying to keep all genes when did gdcDEAnalysis analysis.
My Arguments:
gdcDEAnalysis(counts, group, comparison, method = "limma", n.cores = NULL, filter = FALSE)
But it keep giving me filtered out results, no different from filter=TRUE.
Could you please help me out with it?
Thanks!

Hi,

I was using GDCRNATools to downlaod data fellowing the GDCRNATools Manual . But I get an error as fellow . Can you check for me please? Thank you in advance!

> gdcRNADownload(project.id     = 'TCGA-CHOL', 
+                data.type      = 'RNAseq', 
+                write.manifest = FALSE,
+                method         = 'gdc-client',
+                directory      = rnadir)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") : InternetOpenUrl failed: '安全频道支持出错'

I'm trying to merge RNAseq data which was downloaded from the Web Browser and unzipped to the "RNEseq2". But when I run the code, the error still exists:

rnaCounts <- gdcRNAMerge(metadata = metaMatrix.RNA, path = 'RNAseq2', data.type = 'RNAseq', organized = FALSE)

Error in open.connection(file, "rt") : cannot open the connection
In addition: Warning message:
In open.connection(file, "rt") :
cannot open compressed file 'RNAseq2/e3908da4-f4c8-43b8-b01d-73bd5fafaa96/dbb50b30-9856-4a56-91e1-d31ad106fd48.htseq.counts.gz', probable reason 'No such file or directory'

Can you help me to fix it?

Thank you very much.

I am using the following code to do survival analysis of genes In TCGA BRCA cohort:

survOutput <- gdcSurvivalAnalysis(gene     = rownames(deALL), 
                                  method   = 'coxph', 
                                  rna.expr = rnaExpr, 
                                  metadata = metaMatrix.RNA)

I got the following error message:

Error in round(cox$wald.test, 2) : non-numeric argument to mathematical function

and I can't figure out this problem, Thank you in advance for any suggestions.

I've downloaded all the data correctly and when i get to the merge moment i recive this error

####### Merge RNAseq data #######
rnaCounts <- gdcRNAMerge(metadata = metaMatrix.RNA,
path = rnadir, # the folder in which the data stored
organized = FALSE, # if the data are in separate folders
data.type = 'RNAseq')

############### Merging RNAseq data ################

This step may take a few minutes

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 2 did not have 9 elements

Anyone could help me with this problem ?

I encountered a problem when running the codes of gdcRNAMerge(). Even though I added the “organized=FALSE” to the gdcRNAMerge() function, it still shows Errors as follows:

Error in open.connection(file, "rt") : 无法打开链结
此外: Warning message:
In open.connection(file, "rt") :
无法打开压缩文件'TCGA-STAD/RNAseq/8ce7dcbd-01a6-42d4-9641-2d3e793c7000/cdd88df9-4bd9-40a3-a701-8ea37005e04b.htseq.counts.gz'，可能是因为'No such file or directory'

It would be very helpful if someone can fix it.