User: ipso

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ipso0
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Posts by ipso

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Comment: C: DESeq2: Sequencing depth as confounding factor after size factor normalization
... You were right. The variability is much less when comparing between the libraries with lower depth. It seems that b1, c1 and d1 are highly different from everything else. b2 to a lesser extend also. a2, c2 and d5 maybe as well, but I believe their deviation should be still acceptable.  What could b ...
written 11 months ago by ipso0
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Comment: C: DESeq2: Sequencing depth as confounding factor after size factor normalization
... Of course, here you go:   For me, c1 vs. c6 and d1 vs. d2 look somewhat linearly correlated. b1 vs. b6 however looks in fact quite weird.  ...
written 11 months ago by ipso0
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Comment: C: DESeq2: Sequencing depth as confounding factor after size factor normalization
... Hi Michael, It's data from hematopoietic stem cells. The dataset is already some years old so the depth is really not that great. Still I need to reanalyse it as it has some unique treatment. I wasn't really sure what you meant by plotting the raw counts so I attached some basic density plots of t ...
written 11 months ago by ipso0
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Comment: C: DESeq2: maxCooks not set (NA)
... Thank you Michael, I obviously missed that note! And thank you also for the advice regarding the outlier replacement! :) ...
written 11 months ago by ipso0
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DESeq2: Sequencing depth as confounding factor after size factor normalization
... Hi, I am performing RNA-Seq analysis on a bulk dataset comprising 4 different groups (a, b, c, d) with 5-6 biological replicates per group. When performing QC plotting, I find that PCA and clustering of vst-transformed values identifies some samples as quite different from the others: # Read dds ...
normalization deseq2 pca sizefactors library size factor written 11 months ago by ipso0 • updated 11 months ago by Michael Love25k
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DESeq2: maxCooks not set (NA)
... Hi, I've got a question regarding the Cooks distance calculation in DESeq2.  My dataset consists of 4 groups with 5-6 biological replicates per group. For some exploratory QC plotting I performed the GLM fitting with different design matrices, one with the batch as covariate (dds.bc) and one with o ...
deseq2 dds cooks distance written 11 months ago by ipso0 • updated 11 months ago by Michael Love25k

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