Dear all, 

 

I am analyzing illumina data and I treat a "little" problem. If I use vst
transformation as proposed by Simon Lin and Pan Du for normalization, I have
a problem with interpretation of these values. 

I have 5 clinical groups, from which one is represents controls. If I apply
log2 transformation, I can simply subtract let's say median of control group
from all values and thus obtain a kind of ratio representing the relative
fold change in expression. If the biologists are interested in "real", not
logged expression, I can derive it using the 2^ function to the logarithm of
value of relative fold change (I know this is a bit tricky, but for
informative purposes still usable).

But when using vst, where arcsinh is used, this task is not so simple,
especially for relative fold change in comparison to control.

How do you treat this problem?

 

Thank you very much.

 

Eva

 

*********************************************
Eva Budinská, M.Sc.
Institute of Biostatistics and Analyses
Faculty of Science and Faculty of Medicine
Masaryk University
Kamenice 126/3, 625 00, Brno, Czech Republic
----------------------------
Tel.: +420 549 493 929
Fax.: +420 549 492 855
Mobile: +420 774 206 332
email: budinska@iba.muni.cz
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