Normalizing exonic reads and then log transforming or variance stabilising
0
0
Entering edit mode
A ▴ 40
@a-14337
Last seen 1 day ago
United Kingdom

Hi,

I have raw counts per exon matrix and want to normalize and do a VST or log2 transform without running any differential expression (for downstream usage separate to DE), so I just need the VST/log2 count matrix.

Is it sufficient to simply run estimateSizeFactors on the DEXseq object and then run vstfrom DESeq2 (or log2 + 1) on the normalized counts before exporting to a csv? are there reasons that VST or log transformations might not be appropriate for exon counts?

thank you

DEXSeq • 67 views
ADD COMMENT

Login before adding your answer.

Traffic: 310 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6