Deseq for pairwise comparison among many pairs
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Feng, Shihai ▴ 20
@feng-shihai-6598
Last seen 7.1 years ago
I have two questions related to how to use Deseq. 1) I have total three sample treatments. I am doing pairwise comparison between treatments. I am wondering what sample pool I should use to calcualte SizeFactors and Dispersion. Should I use only the two treatments data that I use in the subsequent nbinomTest step or use all my three sample treatments to calculate SizeFactors and Dispersion. 2) My sample is bacterial that includes chromosome and plasmids, should I study them separately or together ? More specifically, should I run your deseq pipeline independently on chromosome and plasmid or should I combine chromosome and plasmid data first then run your deseq pipeline. thanks, shihai
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@mikelove
Last seen 1 day ago
United States
hi Shihai, We generally recommend users upgrade to DESeq2, which is faster and more sensitive. Additionally, it would make the pairwise comparisons a bit easier. You could use for example: dds <- DESeq(dds) results(dds, contrast=c("treatment","B","A")) results(dds, contrast=c("treatment","C","A")) results(dds, contrast=c("treatment","C","B")) Which would estimate size factors and dispersions using all samples in the first line. The following three lines build results tables contrasting all pairs of the three treatments. I would guess you can run them together, as genes from different chromosomes are combined in a standard analysis. But if I weren't sure, you could compute the size factors from the chromosomes and from the plasmids separately. If these are similar, then I would run them all together. If you have two vectors which identify the plasmid rows and the chromosome rows: estimateSizeFactorsFromMatrix( counts(x)[ plasmidRows, ] ) estimateSizeFactorsFromMatrix( counts(x)[ chromosomeRows, ] ) where x is the dataset, either CountDataSet or DESeqDataSet for DESeq2. Mike On Tue, Jun 10, 2014 at 3:14 PM, Feng, Shihai <sfeng at="" lanl.gov=""> wrote: > I have two questions related to how to use Deseq. > > 1) I have total three sample treatments. I am doing pairwise comparison between treatments. I am wondering what sample pool I should use to calcualte SizeFactors and Dispersion. Should I use only the two treatments data that I use in the subsequent nbinomTest step or use all my three sample treatments to calculate SizeFactors and Dispersion. > > 2) My sample is bacterial that includes chromosome and plasmids, should I study them separately or together ? More specifically, should I run your deseq pipeline independently on chromosome and plasmid or should I combine chromosome and plasmid data first then run your deseq pipeline. > > thanks, > shihai > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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