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Comment: Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low
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Alexander
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Dr. Love,
Thank you for the support. Is there a hard-and-fast rule for choosing a threshold in bulk RNAseq analyses using lfcthreshold()? …
Answer: Pre-filtering, adjusting independent filtering, or lfcthreshold() on DESeq2? Low
by
Michael Love
43k
There are a couple posts on here that also mention this but maybe hard to find: lfcShrink is more aggressive at shrinking that the point nu…
Answer: Which GTF file to use for creation of tx2gene files?
by
Michael Love
43k
I use the top GTF and FASTA from GENCODE. I do not include haplotype chromosomes in the reference.
Answer: DESeq2 LRT: Testing Effects of Treatment1, Treatment2, and Their Interaction in
by
Michael Love
43k
The reduced model depends on what you want to subject to null hypothesis testing. One idea would be to have ChatGPT explain what each full …
Answer: 6 groups to compare DESeq2 (Wald vs LRT)
by
Michael Love
43k
> I get the same number of DEGs in each individual comparison
this is a FAQ in the DESeq2 vignette
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