Hot answers tagged

2 votes

How do I correctly format my limma/eBayes code?

You need to look at how to create a model matrix : In your code, you did not specify the data from which the Sex ...
Basti's user avatar
  • 236
2 votes

How do I fix this limma line?

My guess is you need to index matchedgeneTPM before you run lmFit(), not after: ...
user438383's user avatar
  • 1,621
2 votes

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

There is no direct support for this by best knowledge. Similar questions have been asked previously in the Bioconductor support forum, for example: They ...
ATpoint's user avatar
  • 948
1 vote

Pathway Enrichment Analysis for one specific pathway?

Two questions Significance Lack of consistency between enzymes (log2) within the arginine and proline metabolism pathway. . 1. We've dealt with significance in a past post on Limma (it was not voom ...
M__'s user avatar
  • 11.3k

Only top scored, non community-wiki answers of a minimum length are eligible