[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.

Cheers,
Wei

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 
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



More information about the Bioconductor mailing list