User: Fred

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Fred0
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Posts by Fred

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Comment: C: high lcfSE for genes with zero counts in the majority of conditions
... Hi Michael, I confirm that the gene25047 is not significant using the other approaches you suggested me. I will also try to use design = ~ns(x). Thanks Fred ...
written 22 days ago by Fred0
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Comment: C: high lcfSE for genes with zero counts in the majority of conditions
... Sorry to bother you again. I think something is still missing. Using the command below: dds <- DESeqDataSetFromMatrix(countData = cts, colData = col1, design = ~condition) keep <- rowSums(counts(dds) >= 10) >= ...
written 23 days ago by Fred0
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Comment: C: high lcfSE for genes with zero counts in the majority of conditions
... Great, it worked! Thanks Michael. Fred ...
written 23 days ago by Fred0
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Comment: C: high lcfSE for genes with zero counts in the majority of conditions
... Thanks Michael for your suggestions. First of all, the DEseq2 version I'm using is the DESeq2_1.22.2 and thus not the last one (my fault!). I've updated my DESeq2 version but nothing changes. (Rversion 3.6.1, Platform: x86_64-apple-darwin15.6.0 (64-bit), Running under: macOS High Sierra 10.13.6, ...
written 24 days ago by Fred0
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high lcfSE for genes with zero counts in the majority of conditions
... Hi DESeq2 developers, I have run DEseq2 on a dataset composed by 90 samples (18 different groups x 5 replicates each) and I am interested in the geneA that is known by literature to be highly expressed in 1 group (S04) and has zero counts in almost all the others (attached at the end of the post) ...
deseq2 written 25 days ago by Fred0 • updated 25 days ago by Michael Love25k

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