Can not parse metadata by providing the metadata file. about gdcrnatools HOT 8 OPEN

@thy-chan Hi, could you please tell me the project you are trying to parse? Thanks

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RNA-Seq files in TCGA-BRCA. The format of the metadata file has changed so that the GDCRNATools can't parse it.

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@thy-chan Thank you so much for the reminder. I have just checked the JSON file in GDC and they do have changed the format. There's very little information in the file now, so I recommend that you can parse metadata use the automatic mode (eg., meta <- gdcParseMeta(project.id='TCGA-BRCA', data.type='RNAseq'), and then select the sample you'd like to use. Thanks

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Yes, the information in the GDC's JSON file is reduced. I think the GDC extracts other information separately and puts it in other files, such as the Biospecimen and Sample sheet in the screenshot. Thanks

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Parsing the metadata using the automatic mode for the TCGA-BRCA project does unfortunately not seem to work either:

> metaMatrix <- gdcParseMetadata(project.id='TCGA-BRCA', data.type='RNAseq')
Error in vapply(seq_len(nSam), function(i) null2naFun(metadata[[i]]$cases[[1]]$demographic$gender), :
values must be type 'character',
but FUN(X[[297]]) result is type 'logical'

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I got a same error when parsing TCGA-COAD metadata, here it is:

the command used:

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HI, is this because of my internet problem?
or?
thank you very much

metaMatrix.MIR <- gdcParseMetadata(project.id = "TCGA-LUSC",

•                                data.type  = "miRNAs")
  

Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") : InternetOpenUrl failed: '操作超时'

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I got an error when automatic download RNAseq data, here it is:

the command used:

an error when Merge RNAseq data:

thank you very much

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