[BioC] backgroundCorrect offset value

[Gordon K Smyth]

Dear Prasad,

> Date: Mon, 29 Aug 2011 02:17:01 +0000
> From: Prasad Siddavatam <siddavatam at gmail.com>
> To: <bioconductor at stat.math.ethz.ch>
> Subject: Re: [BioC] backgroundCorrect offset value
>
> 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?

No, I'm not.  All probes should be retained for background correction. 
Non-expressed probes should be filtered before using eBayes().

> 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
> achieved.

There is no maximum value.  Higher is better.

I think you're worrying about this more than is necessary.  A decent value 
like offset=50 will give good results in a wide variety of situations.

You can even use

   fit <- eBayes(fit, trend=TRUE)

which will makes uniformity of the variance less important.  Again, use

   plotSA(fit)

to see what this does.

Best wishes
Gordon

> Appreciate your time and help.
>
> Prasad

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