This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Dexseq: Problem With Constructing An Exoncountset

Hi, Could anyone please help me to solve the problem with making an ExonCountSet? I am new to R, so I am struggling now. I counted the 6 SAM files from GSNAP output using dexseq_count.py by following DEXSeq manual, then I made sample table. Here is what I did:

>sampleTable <- data.frame(row.names = c( "E1", "E2", "E3","F1", "F2", "F3" ), countFile = c( "E1.count", "E2.count", "E3.count", "F1.counts","F2.count", "F3.count" ), condition = c( "E", "E", "E", "F", "F", "F" ))
>sampleTable
countFile condition
E1 E1.count E
E2 E2.count E
E3 E3.count E
F1 F1.counts F
F2 F2.count F
F3 F3.count F
>ecs <-read.HTSeqCounts(sampleTable$countFile,sampleTable,"protein_coding_flattened.gff")
Error in read.table(x, header = FALSE, stringsAsFactors = FALSE) : 
'file' must be a character string or connection*

Thank you very much Thanh

• 3,973 views • link
updated by Irsan Irsan • written by hoangtv • hoangtv

If you type list.files(), do E1.count and the other files show up? Also, I suspect that F1.counts should be F1.count.

• 167 views • link
written by Devon Ryan Devon Ryan

Hi dpryan79, Thank you very much for your quick reply. The F1.counts is just the typo in previous message, sorry about that. Just note that I installed HTseq , flattened the annotation gtf file and did the counting in a different machine and then move data over to another one to process in R. I typed list.files(). All files seem to show up:

list.files() [1] "CITATION" "DESCRIPTION"
[3] "DEXSeq note 11.11.13.odt" "DEXSeq_1.8.0.tar"
[5] "doc" "E1.count"
[7] "E2.count" "E3.count"
[9] "F1.count" "F2.count"
[11] "F3.count" "help"
[13] "html" "INDEX"
[15] "Meta" "NAMESPACE"
[17] "NEWS" "protein_coding_flattened.gff" [19] "python_scripts" "R"

• 0 views • link
written by hoangtv • hoangtv

What is the output of class(sampleTable$countFile)? The common cause of this is that it's not a character vector.

• 123 views • link
written by Devon Ryan Devon Ryan

Just to keep everyone in the loop, Alejandro Reyes (one of the DEXSeq authors) saw this same thread over on seqanswers. The read.HTSeqCounts() function (and vignette) will get tweaked to avoid this error in the future. It's always a good sign with the authors of tools follow these sites and respond when there are issues!

• 0 views • link
written by Devon Ryan Devon Ryan

1 answer

dpryan is right, the class of sampleTable$countFile is factor, it should be character. And F1.counts should be F1.count. Try this:

sampleTable <- data.frame(row.names = c( "E1", "E2", "E3","F1", "F2", "F3" ), countFile = c( "E1.count", "E2.count", "E3.count", "F1.count","F2.count", "F3.count" ), condition = c( "E", "E", "E", "F", "F", "F" ),stringsAsFactors=FALSE)

When you do 

sapply(sampleTables,class)

You will see that both your columns are of type character now.

Proceed with

ecs <-read.HTSeqCounts(sampleTable$countFile,sampleTable,"protein_coding_flattened.gff")
• 219 views • link
written by Irsan Irsan

Log in to answer this question.

More posts like this