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Answer: Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DE
by
James W. MacDonald
64k
The short answer is that you don't. `tximport` is meant to summarize transcript abundance estimates at the gene level, and as you might ima…
Comment: Inconsistent results in DiffBind
by
ATpoint
★
3.6k
One is the "raw" logFCs, not corrected for the standard error of the logFCs, the other one the shrunken logFCs from DESeq2 lfcShrink, "corr…
Answer: Can't download Bioconductor
by
James W. MacDonald
64k
[You need to update][1].
[1]: https://cran.r-project.org/web/packages/BiocManager/vignettes/BiocManager.html#basic-use
Comment: Can't download Bioconductor
by
ATpoint
★
3.6k
Please see especially the 1st and 2nd point in https://www.bioconductor.org/help/support/posting-guide/#keypoints
Comment: Small RNA-seq Analysis DESEQ2 : Unexpected Significance
by
Michael Love
41k
With 3 vs 3, when one sample increases from 50 to 5000, this can lead to rejection of null hypothesis. I'm not surprised with the above cou…
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