[BioC] DESeq2 1.2.10 vs 1.5.26

Ido Tamir tamir at imp.ac.at
Thu Jul 17 17:20:21 CEST 2014


Hi,

I tried to switch from DESeq2_1.2.10 (R3.0) to DESeq2_1.5.26 (R3.1)

but it looks like it 1.5.26 is much more aggressive in the shrinking of the variance estimation.
The rlog normalized fold changes are also very different.

The dataset was generated with 

dds <-  makeExampleDESeqDataSet(n = 30000, m = 6, betaSD = 1.5)

saved and worked on in 2 different R/DESeq2 versions.

a)
Now the obvious question is: is newer truthier?

b)
Is there a parameter to get similar estimates with the new version as in the old version.
Some estimates are more robust now I read in the news e.g. Cooks distance, beta prior variance.
But I don’t understand the large changes this entails for some estimates.


thank you very much,
ido

dispersion estimate plot 3.0
http://postimg.org/image/t3z7i27zz/

dispersion estimate plot 3.1
http://postimg.org/image/v9tickbgf

log fc 3.1 vs 3.0
http://postimg.org/image/mp06le1a7

mean 3.1 vs 3.0 illustrating identical input data (< 100)
http://postimg.org/image/hno76a4fz

mean 3.1 vs 3.0 illustrating identical input data (all)
http://postimg.org/image/wv46qmwan

pvalue 3.1 vs 3.0
http://postimg.org/image/7rn46mynz

3.0:
attr(,"coefficients")
asymptDisp  extraPois
 0.1147892  5.3433952
attr(,"fitType")
[1] "parametric"
attr(,"varLogDispEsts")
[1] 0.9778035
attr(,"expVarLogDisp")
[1] 0.6449341
attr(,"dispPriorVar")
[1] 0.3328694

3.1:
attr(,"coefficients")
asymptDisp  extraPois
 0.1117856  5.8477354
attr(,"fitType")
[1] "parametric"
attr(,"varLogDispEsts")
[1] 0.7119179
attr(,"expVarLogDisp")
[1] 0.6449341
attr(,"dispPriorVar")
[1] 0.25



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