Covariate remove from Expressionset using SVA to yield transformed_expressionset
1
0
Entering edit mode
6.6 years ago

This may be a naive question but I am fairly new to bioinformatics and R in general.

I need to perform eQTL analysis using GGtools and I am attempting to make a smlSet (genotype matrix + expressionset) using functions in GGtools. Is there a way I can correct my expressionset using SVA to generate a transformed expressionset directly as opposed to the typical workflow which uses the matrix output from SVA to perform linear regressions via limma() or a similar function.

Sorry if this seems simple but perhaps I am simply missing something simple.

sva ggtools eqtl expressionset limma • 1.4k views
ADD COMMENT
1
Entering edit mode
6.6 years ago

Actually, I found the answer to my question in another post:

Remove Surrogate Variables and Batch

ADD COMMENT

Login before adding your answer.

Traffic: 1973 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