User: HD

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HD0
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Posts by HD

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Comment: C: Suggestions for avoiding False Positives while identifying differentially expres
... OK. Thanks Michael I will give a try at SAMseq. ...
written 3 months ago by HD0
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Comment: C: Suggestions for avoiding False Positives while identifying differentially expres
... Result from lfcShrink is as follows: dds<-batch.filter dds$stability <- factor(dds$stability, levels = c("stable","unstable", "host")) design(dds) <- ~ stability DDS_batch <- DESeq(dds) res<-lfcShrink(DDS_batch, coef="stability_unstable_vs_stable", type="apeglm") ...
written 3 months ago by HD0
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Comment: C: Suggestions for avoiding False Positives while identifying differentially expres
... So here is what I did... I don't understand why I don't see unstable_vs_stable condition listed in resultsNamesDDS. But counts are as mentioned below. A gene is being reported DE based on high counts in B3, D1 and F3 while comparing stable and unstable. #Create input for DE analysis bat ...
written 3 months ago by HD0
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Comment: C: Suggestions for avoiding False Positives while identifying differentially expres
... Thanks for your response Michael. But my problem is not with filtering the raw count matrix. I use the same before moving ahead to differential expression analysis. When I call differentially expressd genes in group of stable (**9** samples = 3 **stable** with all 3 replicates each) vs unstable (an ...
written 3 months ago by HD0
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Suggestions for avoiding False Positives while identifying differentially expressed genes with more than 3 samples per group
... Hi, I have RNA seq data with the samples defined as follows: **ID level stability type** A1 med unstable exp A2 med unstable exp A3 med unstable exp B1 med stable exp B2 med stable exp ...
deseq2 written 3 months ago by HD0 • updated 3 months ago by Michael Love26k

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