Help with DESeq please

[Name_less_]

Hello everyone
I am new in the use of DESeq and I have problems for obtain Diferencial Expression of an Output of EDGE-Pro.
In R, I followed the steps on this page:

https://wikis.utexas.edu/display/bio...ssion+analysis

In where are the next steps:

login1$ R
...
> library("DESeq")
> counts = read.delim("gene_counts.tab", header=F, row.names=1)
> head(counts)
> colnames(counts) = c("wt1", "mut1", "wt2", "mut2")
> head(counts)
> my.design <- data.frame(row.names = colnames( counts ),condition = c( "wt", "mut", "wt", "mut"), libType = c( "single-end", "single-end", "single-end", "single-end" ))
> conds <- factor(my.design$condition)
> cds <- newCountDataSet( counts, conds )

BUT, in this point, I have the next error:

Error en round(countData) : non-numeric argument to mathematical function

Someone can help me? please

My file is the next (the firsts five lines):

gene 571A.rpkm_0 571B.rpkm_0 571C.rpkm_0 571D.rpkm_0
geneA 406 609 423 477
geneB 67 117 76 64
geneC 21134 18099 14720 14153
geneD 810 857 725 691

Each 571 is one condition, without replicates.

[edm1]

Is counts formatted correctly, does

head(counts)

look like you'd expect?

Is there a reason you are not using DESeq2? In DESeq2 you'd use DESeqDataSetFromMatrix instead of newCountDataSet:

dds <- DESeqDataSetFromMatrix(countData = counts,
                              colData = my.design,
                              design = <formula>)

You should follow the PDFs available here:

http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html

[Name_less_]

The table looks as expected, but I will try of use DESeq2. However, still I can not solve this problem in DESEQ.

[evozoa]

Check to make sure your sample and gene names do not include spaces. If they do, it will throw off the column numbers.

[Name_less_]

Hi
Finally I used DEseq2 and I could get what I expected. Thanks for all and greetings !!