edger and deseq2 log2FC nornalization
1
0
Entering edit mode
tonja.r ▴ 80
@tonjar-7565
Last seen 8.1 years ago
United Kingdom

In the Microarray if the data is not center around 0 on MA-plots, it is normalized with LOESS. I was not able to find if edgeR performs something like loess normalization for log2Fold changes as it seems that the values are always centered around zero.

deseq2 edger • 1.3k views
ADD COMMENT
0
Entering edit mode

I think you may have accidentally deleted half of your question.

ADD REPLY
2
Entering edit mode
@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…

The centering of estimated log fold changes around zero is a consequence of the estimation of the size factors (as they are called in DESeq2) or normalisation factors (edgeR).

The kind of non-linear operations on microarray data as entailed by loess-fitting in the MA-plot are motivated by non-linearities in the data, like scanner saturation and background fluorescence. These effects do not appear in decent RNA-Seq data and the authors of edgeR and DESeq2 have not seen a need for introducing such non-linear fudges.

ADD COMMENT

Login before adding your answer.

Traffic: 526 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