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$condition)
> cds <- newCountDataSet( counts, conds )
BUT, in this point, I have the next error:
Error en round(countData) : non-numeric argument to mathematical function
Someone can help me? please
My file is the next (the firsts five lines):
gene 571A.rpkm_0 571B.rpkm_0 571C.rpkm_0 571D.rpkm_0
geneA 406 609 423 477
geneB 67 117 76 64
geneC 21134 18099 14720 14153
geneD 810 857 725 691
Each 571 is one condition, without replicates.
I am new in the use of DESeq and I have problems for obtain Diferencial Expression of an Output of EDGE-Pro.
In R, I followed the steps on this page:
https://wikis.utexas.edu/display/bio...ssion+analysis
In where are the next steps:
login1$ 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.
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