Metadata sheet for DEXSeq analysis
0
0
Entering edit mode
A ▴ 40
@a-14337
Last seen 11 months ago
United Kingdom

Hi all, 

Just wondering if  anybody can offer some help. I have searched for this answer but unfortunately have not found any solutions

I am currently looking at an aging population of a specific cell type in various organs and am interested in looking for differential isoform usage over time. 

I have created a Granges object using the summarizedoverlap function for exon counting.and want to call the DEXSeq function. However, according to the vignette, I need to add the colData$ manually, but I have 95 samples, all of which contain different organs and 4 different time points (and soon these will be doubled, and further time points included).

Is there a way of assigning the sampledata sheet that I use for the DESeq pipeline to the summarized experiment output in order to call the Dexseq function to identify the samples and their respective time points, and then use ~time_point + Organ+ exon as the design?

Many thanks for all of your help!

dexseq differential isoform usage isoforms summarizeoverlaps granges • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 941 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