User: bioinfo

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Posts by bioinfo

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Comment: C: DESeq2- multifactor design- 3 conditions and 3 timepoints
... Thanks, Michael for confirming the design. I got confused with resultsNames(dds), thinking that it would provide all the possible comparisons. This post made things more clear: https://support.bioconductor.org/p/98346/ Thanks! ...
written 8 months ago by bioinfo0
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DESeq2- multifactor design- 3 conditions and 3 timepoints
... Hi All, I am trying to generate a design for my RNA-seq data and I am not able to get the right comparison. This is my sampleTable: ``` sampleName condition time Mock12hRep1 Mock12h 12 Mock12hRep2 Mock12h 12 Mock12hRep3 Mock12h 12 Mock3hRep1 ...
deseq2 design written 8 months ago by bioinfo0 • updated 8 months ago by Michael Love25k
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Comment: C: Batch-effect: batch in design and corrected batch with sva- DESeq2
... Thanks, Michael for the answer. I was not sure why I am getting such different numbers. I would go ahead with ~ batch + condition. Also when I use n.sv = 2 and use only two SVs I only get 4 DE genes. Is it recommended to use high n.sv or low n.sv when running svaseq. Any suggestion? ...
written 9 months ago by bioinfo0
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Batch-effect: batch in design and corrected batch with sva- DESeq2
... Hi All, I did DESeq2 on my set of samples and I got only two DE genes. When I checked I found that my samples were collected at different time points and in PCA a prominent batch effect is shown. So, I included a batch in my design ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sample ...
deseq2 svaseq written 9 months ago by bioinfo0

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