[BioC] filtering Illumina data

Sean Davis sdavis2 at mail.nih.gov
Wed Aug 20 22:19:37 CEST 2008

On Wed, Aug 20, 2008 at 4:09 PM, Lana Schaffer <schaffer at scripps.edu> 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?

I would definitely not use ALL the arrays in your cutoff.  Perhaps
having 10-20% of samples detected for a given probe is more
appropriate.  If you force all arrays to meet detection cutoffs, you
are excluding potentially interesting probes that are "on" in some
subset, but "off" in another.  An alternative is to filter by
variation (cv, for example).


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