[BioC] filtering Illumina data

Wei Shi shi at wehi.EDU.AU
Thu Aug 21 01:29:25 CEST 2008

Hi Lana:

   An alternative way is to remove those probes which are not changing 
across all samples after your data is normalized. You may draw a mean vs 
sd plot (mean and standard deviation for each probe across all samples) 
to determine a reasonable sd threshold for the filtering.

   Hope this helps.


Lana Schaffer wrote:
> Hi,
> I have filtered Illumina data from 46,633 probes to 6537 probes
> using the Detection Pval.  I used a cutoff of .05 to call
> detection across all the arrays.  
> Can someone tell me if this is reasonable?
> What is a better way of filtering?
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu 
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