[BioC] LIMMA P-value calculations/Suggestions for flagged data

[Gordon K Smyth]

Dear Sergio,

Yes, RMA and gcRMA avoid a blowout of variability at low intensities.  In fact they are very
aggressive algorithms in this regard.

Note: you still might filter low intensities probes in some circumstances, but you need to remove
entire probes, entire data rows, not individual data values.  Filtering individual spots or
individual cells on intensity doesn't make sense to me.

Best wishes
Gordon

> Date: Fri, 23 Mar 2007 18:40:59 -0800 (PST)
> From: "Sergio Barberan" <barberan at biology.ucsc.edu>
> Subject: Re: [BioC] LIMMA P-value calculations/Suggestions for flagged
> 	data
> To: bioconductor at stat.math.ethz.ch
>
>> I've argued on this mailing list and elsewhere for a long time that,
>> rather than flagging faint
>> spots, it's better to use a better background correction method that
>> avoids a blow out of M-values
>> at low intensities.
>
> Is RMA such a good background correction method?
>
> cheers,
> sergio