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Answer: Deseq2 Design
by
James W. MacDonald
67k
Trying to use a conventional factor analysis, particularly if you are new, is not the way to go (I have been doing this for over 20 years n…
Answer: p value is 0, padj is 0
by
swbarnes2
★ 1.4k
I think the default smallest value R will return is 1x10^-300. So I'd take a look at the counts, and see if it makes sense that the p-valu…
Comment: p value is 0, padj is 0
by
Michael Love
43k
``` > set.seed(1); t.test(rnorm(200,rep(c(0,80),each=100)) ~ rep(0:1,each=100))$p.value [1] 0 ```
Answer: Cannot install GO.db and org.Hs.eg.db
by
James W. MacDonald
67k
You might try tracing the namespace loading. ``` Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2") install("org.Hs.eg.db") ``` And see if th…
Answer: p value is 0, padj is 0
by
James W. MacDonald
67k
It is quite possible for a very small p-value to remain very small after multiplicity adjustment. I don't know the cutoff for `DESeq2` to r…
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Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2
Answer: Mapping Between GenBank ID's and Uniprot
Comment: What type of counts data to import for performing Isoform analysis in edgeR
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