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Error in running diffcoexp

2 messages · Dr Priyanka Jain, PIKAL Petr

#
Dear Sir/ Madam,
                             I am getting the following error:


geneExp <- read.table("DV_control_FPKM.txt",header=T, sep="\t",row.names=1)
geneExp=as.matrix(as.data.frame(geneExp))
head(geneExp)
geneExp2 <- read.table("DV_introgressed_line_FPKM.txt",header=T,
sep="\t",row.names=1)
geneExp2=as.matrix(as.data.frame(geneExp))
head(geneExp2)
library(diffcoexp)
allowWGCNAThreads()
res=diffcoexp(exprs.1 = geneExp, exprs.2 = geneExp2, r.method = "spearman" )
Error in exprs.1[rownames(exprs.1) != "", ] :
  incorrect number of dimensions

I have attached my input file along with mail
-- 
With Regards,
*Dr Priyanka Jain (PhD)*,
Mobile : 9718854136
1 day later
#
Hi.

See inline
already data frame
so as.data.frame unnecessary
better str(geneExp) to see actual structure
)
My guess is that during fiddling with as.data.frame and matrix your data are
not complient with the function
"a SummarizedExperiment, data frame or matrix for condition 1, with gene IDs
as rownames and sample IDs as column names"
No (or almost no) attachments allowed. Better using dput for sharing data.

Cheers
Petr