Hello guys,

Any help will be appreciated.

I am trying to use the function samWrapper from the new version of the DEGseq package. The exact same code works well for the data supplies in the tutorial, but not with my data. It gives me the following error:

Error in cat(list(...), file, sep, fill, labels, append) : 

  argument 2 (type 'list') cannot be handled by 'cat'

My code is as follows:

library ("DEGseq")
geneExpFile <- read.delim("/Users/juanjovel/temp/microbiome/myData_nonNorm.txt", 
                          row.names="miRNA", sep="\t")
write.table(geneExpFile[1:100,])
set.seed(100)
geneExpFile1 <- geneExpFile
geneExpFile2 <- geneExpFile
output <- file.path(tempdir(), "samWrapperOut.txt")
expCol1=c(2,4,6,8,10,12,14,16,18,20,22,24)
expCol2=c(3,5,7,9,11,13,15,17,19,21,23,25)
measure1=c(-1,-2,-3,-4,-5,-6,-7,-8,-9,-10,-11,-12)
measure2=c(1,2,3,4,5,6,7,8,9,10,11,12)
samWrapper(geneExpFile1=geneExpFile1, geneCol1=1, expCol1=expCol1, measure1=measure1,
           geneExpFile2=geneExpFile2, geneCol2=1, expCol2=expCol2, measure2=measure2,
           nperms=100, min.foldchange=2, max.qValue=1e-4, output=output, paired=TRUE)

Hi there

I had a similar problem as long as I imported my dataset .txt files using either read.table or read.csv or something like that.

Whe I import my data as matrices I can get it running eg.

geneExpMatrix1 = readGeneExp('inputfile.txt', header=FALSE, sep='', geneCol=1, valCol=2)

Good luck