Some errors have slipped into the tutorial, making some commands not usable with a simple Copy-Pasting.
Here is a list of some of which I have found, assigned by categories:
Issue 1:
No folder "data-raw" can be found in deconICA package from R. It is present in the GitHub repository but during the installation in R, the folder is not present.
Some commands to not work, such as:
GE_SDY420 <- read.delim("./data-raw/xCell_ImmPort/GE_SDY420.txt", row.names=1, stringsAsFactors=FALSE)
FACS_SDY420 <- read.delim("../data-raw/xCell_ImmPort/FCS_SDY420.txt", row.names=1, stringsAsFactors=FALSE)
TIMER <- ACSNMineR::format_from_gmt("./data-raw/TIMER_cellTypes.gmt")
data(BEK_ica_overdecompose)
Issue 2:
When assigning metagenes, the whole matrix should be given as input without the "$r".
This is only found in the html version of the tutorial (not the Rmd one).
Here are the cases where this happens:
mix1.assign.20 <- assign_metagenes(mix1_corr.basis.20$r, exclude_name = NULL)
GE_SDY420_ica_39.LM22.reciprocal.corr <- assign_metagenes(GE_SDY420_ica_39.corr.LM22$r, exclude_name = NULL)
reciprocal.corr <- assign_metagenes(corr$r, exclude_name = NULL)
reciprocal.corr.Biton <-assign_metagenes(corr_Biton$r, exclude_name = c("M8_IMMUNE", "M2_GC_CONTENT"))
Issue 3:
When using "kable", no import has been stated prior to the usage, creating an error.
library(kableExtra) should be mentioned at some point in the tutorial.
Issue 4:
When generating html tables with "kable", the command to visualise the table in Rstudio should be added as some cases lack it. For instance, the line
kable(GE_SDY420_ica_39.LM22.reciprocal.corr, "html", row.names = FALSE)
should become
kable(GE_SDY420_ica_39.LM22.reciprocal.corr, "html", row.names = FALSE) %>% kable_styling(font_size = 8)
Issue 5:
Some typos here and there are hidden. Here would be the needed correction imo:
cell_prop <- pData(GSE64385)[ , c(1, 2, 10, 11,12, 13, 14, 15, 16, 17)]
overdecompose parameter that selects number of composed components? needed to perform overdecomposition of the input matrix
An efficient way to in interpret a component is to use correlation with some known profile or as we call it a
type (a metagene), we can then correlate them with obtained components and verify if some of decomposed
They can be considered as a negative control.
#without endothelial cells and Fibroblasts