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Old 10-09-2014, 05:14 AM   #1
Name_less_
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Location: Chile

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Default Help with DESeq please

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.
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Old 10-09-2014, 05:43 AM   #2
edm1
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Location: UK

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Posts: 10
Default

Is counts formatted correctly, does
Code:
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:

Code:
dds <- DESeqDataSetFromMatrix(countData = counts,
                              colData = my.design,
                              design = <formula>)
You should follow the PDFs available here:
http://www.bioconductor.org/packages...ml/DESeq2.html
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Old 10-09-2014, 08:43 AM   #3
Name_less_
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Default

The table looks as expected, but I will try of use DESeq2. However, still I can not solve this problem in DESEQ.
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Old 10-20-2014, 09:57 AM   #4
evozoa
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Default

Check to make sure your sample and gene names do not include spaces. If they do, it will throw off the column numbers.
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Old 10-27-2014, 06:03 AM   #5
Name_less_
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Default

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