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 10-09-2014, 05:14 AM #1 Name_less_ Member   Location: Chile Join Date: Oct 2014 Posts: 12 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.
 10-09-2014, 05:43 AM #2 edm1 Member   Location: UK Join Date: May 2013 Posts: 10 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 = )``` You should follow the PDFs available here: http://www.bioconductor.org/packages...ml/DESeq2.html
 10-09-2014, 08:43 AM #3 Name_less_ Member   Location: Chile Join Date: Oct 2014 Posts: 12 The table looks as expected, but I will try of use DESeq2. However, still I can not solve this problem in DESEQ.
 10-20-2014, 09:57 AM #4 evozoa Junior Member   Location: alabama Join Date: May 2014 Posts: 1 Check to make sure your sample and gene names do not include spaces. If they do, it will throw off the column numbers.
 10-27-2014, 06:03 AM #5 Name_less_ Member   Location: Chile Join Date: Oct 2014 Posts: 12 Hi Finally I used DEseq2 and I could get what I expected. Thanks for all and greetings !!