Bioconductor FactoMineR

Showing : FactoMineR • reset

1

vote

3

replies

642

views

Biplot FactoMineR proteomics PCAtools ellipse

updated 8 months ago by Kevin Blighe 3.8k • written 8 months ago by M Tuhin • 0

0

votes

1

reply

1.6k

views

clustering r fpc FactoMineR

4.2 years ago anahochmanova • 0

4

votes

6

replies

1.2k

views

deseq2 factominer PCA

updated 7.2 years ago by Ryan C. Thompson 7.8k • written 7.2 years ago by sebastiano.curreli • 0

0

votes

5

replies

3.9k

views

software error factomineR bioclite

updated 8.4 years ago by Martin Morgan 25k • written 8.4 years ago by dany_wm44 • 0

4 results • Page 1 of 1

Recent ...

Replies

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

Votes

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

Answer: Batch correction and repeated measures

Awards • All

Popular Question to James W. MacDonald 63k