[BioC] backgroundCorrect offset value

Prasad Siddavatam siddavatam at gmail.com
Mon Aug 29 04:17:01 CEST 2011

Dear Dr. Smyth,

Thank you very much for your detailed response. I am going to read the 
references. I understand why I am getting more differential genes with bigger 
offset value. Basically we are bringing the variance close to zero (with more 
uniformity across probes).

Are you suggesting to delete the probes before doing the background correct?
If yes, is there any limit on the maximum number of probes to be deleted?

In the variance stabilization, which maximum value (approximately) of 
fit$df.prior is considered high enough to call a good variance stabilization is 

Appreciate your time and help.


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