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Comment: Can VST-transformed community composition data be expressed as relative abundanc
Thank you for your fast and helpful clarifications. I must have understood the pseudo-counts wrong (the video episode CC195 of the Riffomo…
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
limma already adjusts for the baseline expression level of each subject. Trying to include baseline expression explicitly in the linear mod…
Comment: Remove duplicate genera in DEseq output?
This seems to be very specific rather than a general and technical DESeq2 question. See the last point of https://support.bioconductor.org/…
Comment: Use with_go along with other filters in getBM function
Hi @mike-smith , you are correct. I was trying to select the ones that have some GO annotations by using the `with_go` filter. I was confus…
Answer: Can VST-transformed community composition data be expressed as relative abundanc
The point of the VST is to make the data systematically homoskedastic (that is, not systematic trend of variance over mean, but not e.g. fo…
A: VariantAnnotation non-model species
A: Using R package 'limma' on pre-normalized counts and the effect of non-equivalen
Using R package 'limma' on pre-normalized counts and the effect of non-equivalent reads/sample on limma linear model
A: What can I do if I only have TPM but not raw counts data?
What can I do if I only have TPM but not raw counts data?
James W. MacDonald
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