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sigurd.krieger
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@8166e2fd
Last seen 4.7 years ago
Hi there, I want analyse a dataset of several cell lines (J82,SW870) vs treatments (Ctrl, Cis, Tala) with DeSeg2. As design I use ~celllines+treatment, after running DeSeq2 I need to isolate the DEGs within a treatment vs. control like results(vst, contrast=c("treatment","Ctrl","Cis")). Is there a correct way to isolate the DEGs just only for one celltype like J82.
I started with isolating a subset of the DeSeg2 object like dds <- dds[,dds$cellline == "J82"] and doing vst() from where I get the siginificant regulated genes by filtering on logFC and padj. Can I do this or do I disturb anything inside the DeSeq2 object ? Or is there a better way to do this ?
Thank you for you advise Sigurd
Thank you for your answer and helping with my ignorance. Sorry not to mention the replicates, of course we have triplicates for each celltype/treatment. But how would I set the result contrast to get for example the treatment DEG Ctrl vs. Cis of the cell line J82 ?
As far as interpretation of model terms, I would recommend to first look over the vignette section on interactions, and then for further questions, I would suggest working with a statistician or someone familiar with linear model terms. The designs and contrasts are not specific to DESeq2 but used throughout R packages for linear models.