Conumee output as input for Gistic2.0
0
0
Entering edit mode
12 months ago
sativus ▴ 20

Hi Biostars!

I am currently undertaking a CNA-analysis, in which i have access to methylation array data (Infinium EPIC). After generating CNV data through conumee, i would like to use this output for further processing using Gistic 2 to study CNAs at a gene level. The documentation of gistic states that in the input file for the Seg.CN column, it requires (log2() -1 of copy number) for each segment. This to my understanding is the same value as the "segment_mean" column in the conumee output (as it represents the log2 ratio of the intensity of group X compared to the intensity of group Y).

My question is thus, am i correct in making the assumption that the values found in the segment_mean column in the conumee output, can be used directly as values for the Seg.CN column as input for Gistic 2?

cnv copy gistic cna conumee • 390 views
ADD COMMENT

Login before adding your answer.

Traffic: 1562 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