Bioconductor Spatiallibd

Showing : spatiallibd • reset

vote

424

views

spatialLIBD

updated 13 months ago by Leonardo Collado Torres ★ 1.0k • written 13 months ago by kstern • 0

votes

replies

725

views

spatialLIBD

updated 13 months ago by Leonardo Collado Torres ★ 1.0k • written 13 months ago by kstern • 0

votes

447

views

spatialLIBD

updated 19 months ago by Leonardo Collado Torres ★ 1.0k • written 20 months ago by Ma • 0

votes

550

views

spatialLIBD

updated 2.2 years ago by Leonardo Collado Torres ★ 1.0k • written 2.2 years ago by Dimitri • 0

votes

replies

565

views

biorxiv spatialLIBD News

3.6 years ago Leonardo Collado Torres ★ 1.0k

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