User: bge

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bge0
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Posts by bge

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Comment: C: DESeq2 normalization and group-wise or pair-wise comparisons
... Hi Michael, Regarding the together versus split question, thank you for pointing out the shrinkage dependence on the number of analyzed samples. I am looking at plotDispEsts() plots for analyses of tissue subsets and I was confusing the effects of within-group variability and the number of tissues. ...
written 13 days ago by bge0
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Comment: A: DESeq2 normalization and group-wise or pair-wise comparisons
... Hi, I had made a PCA plot and saw that replicates of most tissues cluster reasonably well but the replicates that belong to two tissues spread across about half of the vertical extent of the plot. I know that this is bad, it distorts the 'globally' calculated dispersion values. Is there an objectiv ...
written 14 days ago by bge0
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DESeq2 normalization and group-wise or pair-wise comparisons
... Hi, I have data for 26 different tissues and I want to perform exhaustive pairwise comparisons between them. I want to find normalized expression levels for the samples and differentially expressed genes between tissues. For both I intend to use DESeq2. From my reading and testing, I believe that ...
deseq2 written 15 days ago by bge0
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Comment: C: DESeq2 comparison of sample combinations
... Hi Michael, I am grateful for your reassurance and advice. Thank you. Brent Ewing ...
written 11 weeks ago by bge0
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Comment: C: DESeq2 comparison of sample combinations
... Hi Michael, Thank you for clarifications and corrections. I fear that I may have mislead you with my description of the samples. The phrase, 'the cell types belong to one of two organ classes', was not meant to suggest a special relationship between any cell type in organ 1 and cell type in organ ...
written 12 weeks ago by bge0
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DESeq2 comparison of sample combinations
... Hi. I am preparing to run DESeq2 on samples and I am uncertain about how I might proceed. My questions may be elementary: I am not a statistician and have not used R for statistical modeling or DESeq2 for differential expression analyses. We have biological samples each of which consists of RNA f ...
deseq2 written 3 months ago by bge0 • updated 3 months ago by Michael Love15k

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