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runDREEP was displayed error information--argument specifying columns received non-existing column(s): cols[1]='pathway' #5

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SSSJe opened this issue Oct 23, 2024 · 0 comments

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@SSSJe
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SSSJe commented Oct 23, 2024

There is a error in processing the drug analysis when I run runDREEP using DREEP R package.

data <- gficf(M=dat,verbose = T) # dat is a count matrix

dreep.data <- DREEP::runDREEP(M = data$gficf,cores=4,
  n.markers = 500,
 gsea = "simple",
gpds.signatures = c("CTRP2","GDSC"))

Process massage is as follows:

10:44:43 Loading GPDS signatures..
processing [========================] 2/2 (100%) [eta: 0s]
10:44:44 Extracting top scoring genes from each cell..
processing [========================] 5/5 (100%) [eta: 0s]
10:44:53 Running DREEP...

Error massage is as follows:

Error in checkForRemoteErrors(val):
4 nodes produced errors; first error: argument specifying columns received non-existing column(s): cols[1]='pathway'

the data$gficf is process from the seurat object, which is a count matrix (row is cells, column is genes). The data (dat) form is as follows:
image

And the data of data$gficf is composed of (as follows):
image

I don't know how to check for errors, what's wrong with that??
Is it because of the lack of column names in the data$gficf?
Looking forward to your reply~ Thx... T_T

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