[BioC] filtering Illumina data

Paul Leo p.leo at uq.edu.au
Thu Aug 21 02:15:05 CEST 2008


I typically use the lumi package where the default is <0.01 and only
probes which are below this dectection threshold in all samples are
deleted. This typically leaves between 14K to 16K of genes. 7000 genes
is perhaps a little too aggressive. Illumina *I think* recommends a Th
of .01 too (though be careful when you export the probe profiles it
sometimes converts these to 1-Th.
Cheers
PAul


-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Wei Shi
Sent: Thursday, August 21, 2008 9:29 AM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] filtering Illumina data

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 
>
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