User: rmash

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rmash0
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Posts by rmash

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Comment: C: DESeq2 - controlling for block vs analysing blocks separately and lfcShrink chan
... Ok that makes more sense re thresholds. Re: rankings I was just curious what your inclination would be -- as one could do it in a simple way (literally ranking and looking at if there is overlap) or doing something more heavy duty (rank-rank hypogeometric mean testing) across the 2 blocks. Thanks ...
written 4 weeks ago by rmash0
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Comment: C: DESeq2 - controlling for block vs analysing blocks separately and lfcShrink chan
... Thanks for the advice! 1) So which p-values should I be going by? [This][1] tutorial had me confused. "NOTE: Shrinking the log2 fold changes will not change the total number of genes that are identified as significantly differentially expressed. The shrinkage of fold change is to help with downstr ...
written 4 weeks ago by rmash0
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DESeq2 - controlling for block vs analysing blocks separately and lfcShrink changes the DE genes drastically
... I have an experiment which I did in blocks (week 1 vs week 2) and 4 groups (A, B, C and D). My understanding is that I can do the analysis controlling for block by doing this. dds_results <- DESeqDataSetFromMatrix(countData = genes.matrix, colData = ...
deseq2 written 4 weeks ago by rmash0 • updated 4 weeks ago by Michael Love25k

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