Error in running diffcoexp
Hi. See inline
-----Original Message-----
From: R-help <r-help-bounces at r-project.org> On Behalf Of Dr Priyanka Jain
Sent: Wednesday, September 2, 2020 1:12 PM
To: r-help at r-project.org
Subject: [R] Error in running diffcoexp
Dear Sir/ Madam,
I am getting the following error:
geneExp <- read.table("DV_control_FPKM.txt",header=T,
already data frame
sep="\t",row.names=1) geneExp=as.matrix(as.data.frame(geneExp))
so as.data.frame unnecessary
head(geneExp)
better str(geneExp) to see actual structure
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
My guess is that during fiddling with as.data.frame and matrix your data are not complient with the function
From help page
"a SummarizedExperiment, data frame or matrix for condition 1, with gene IDs as rownames and sample IDs as column names"
I have attached my input file along with mail
No (or almost no) attachments allowed. Better using dput for sharing data. Cheers Petr
-- With Regards, *Dr Priyanka Jain (PhD)*, Mobile : 9718854136 -- With Regards, *Dr Priyanka Jain (PhD)*, Mobile : 9718854136
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