Question

DESeq without nornalization

0

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8.4 years ago

zamanys4 ▴ 10

I am working on a pre-processing method for differential expression analysis, and need to run DESeq method without normalization of input counts. I know that estimateSizeFactors function calculates the scaling factors and I guess estimateDispersions uses them. Is there anyway to bypass normalization in DESeq?

rna-seq • 3.3k views

ADD COMMENT • link updated 8.4 years ago by Devon Ryan 104k • written 8.4 years ago by zamanys4 ▴ 10

score 5 · Accepted Answer · 2015-11-26

5

Entering edit mode

8.4 years ago

Devon Ryan 104k

Just use the sizeFactors() accessor and set everything to 1.

ADD COMMENT • link 8.4 years ago by Devon Ryan 104k