Hello,

Last Friday I was working with UPC and everything went fine, I have several tsv files in the format that is described in the documentation, genes in column 1 and raw counts in column 2.

Today I made a few adjustments in my code and rerun the analysis, but suddenly the returned object is transposes. My gene names are the column names and the input file(s) are in the rows.

From the documentation I should get this:

"Value

An ExpressionSet object that contains a row for each probeset/gene/transcript and a column for each input file."

For unknown reasons this also caused the "as.matrix()" function to crash which I used on the ExpressionSet object.

The function I'm calling: exp <- UPC_RNASeq("prova.txt", ignoreZeroes = T)

Shell:

head prova.txt
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/10002981-10010032>"    0
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/10003486-10045559>"    15
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/10007376-10007694>"    2
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100111499-100160097>"    45
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100163798-100164734>"    0
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100174259-100232187>"    2
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100250296-100250441>"    0
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100257218-100257309>"    0
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/10027439-10027516>"    0
"<http://gbol.life#Homo_sapiens_assembly19/contig/1/gene/100295021-100295093>"    0

I talked to Guus offline. It turned out the inconsistent behavior was likely due to using as.matrix() to extract UPC values from the ExpressionSet object rather than exprs().

exp <- exprs(UPC_RNASeq("prova.txt", ignoreZeroes = T))