Bioconductor R3cseq

Showing : r3cseq • reset

vote

423

views

r3cseq bam trimmed

3.4 years ago ch_el ▴ 10

votes

883

views

r3Cseq

updated 6.3 years ago by izzy.yichao.cai ▴ 10 • written 7.5 years ago by manduchi ▴ 10

votes

replies

708

views

4Cseq r3cseq

7.1 years ago tlgolan • 0

votes

replies

833

views

r3cseq 4c

8.2 years ago Theo • 0

votes

replies

703

views

r3Cseq

8.4 years ago felix.klein ▴ 150

5 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