DiffBind scoreCol value question
1
0
Entering edit mode
erbrocato • 0
@dfeb9251
Last seen 4 months ago
United States

Hi,

I had a question about which values to use for the scoreCol when generating a dba object in DiffBind. My peak files are SICER islandSummary files, which contain columns for pvalue, fold change, and FDR. Currently, I have the scoreCol in my sample sheet set as "sicer" which is pulling the fold change values from my peak files (column 8). Is it best to use fold changes as input into DiffBind, or would pvalues or FDR be a better score to use?

Thanks for your help,

Emily

DiffBind ChIPSeq chipseq • 247 views
ADD COMMENT
1
Entering edit mode
Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 6 days ago
CRUK, Cambridge, UK

In most DiffBind analyses, the initial peaks scores aren't used for anything important. These scores are only used for making plots prior to calling dba.count() (for example, clustering or heatmaps). Once you have called dba.count(), the scores are all based on actual counts and the initial scores are ignored.

ADD COMMENT

Login before adding your answer.

Traffic: 249 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