edger and deseq2 log2FC nornalization
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tonja.r ▴ 80
@tonjar-7565
Last seen 8.0 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 • 1.2k views
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I think you may have accidentally deleted half of your question.

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@wolfgang-huber-3550
Last seen 10 weeks 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.

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