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Answer: after calcNormFactors with EdgeR, how to get TMM normalized matrix?
by
Gordon Smyth
45k
There's no such thing as a "TMM normalized matrix" or "normalized values" in edgeR. Have you read the edgeR User's Guide for how analyses a…
Answer: different results in DESeq2 when comparing groups in two ways
by
James W. MacDonald
59k
If you fit a model using all your data, you will have more degrees of freedom for estimating variability, which will tend to increase power…
Answer: Quantile Normalization after rma or not?
by
James W. MacDonald
59k
You already quantile normalized when you ran `oligo::rma`, so you should not normalize a second time.
Answer: Using featureCounts and downloading Rsubread
by
James W. MacDonald
59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package.
```
BiocManager::install("Rsubread")
library(…
Comment: featureCounts: 0% successfully assigned fragments
by
KMS
•
0
Dear ATpoint
I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count
feature count giving me 0% s…
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