[BioC] Detection slot - Lumi

[Pan Du]

Hi Yogi,

The detection rate is in the normal range and it depends on the biological
samples. Actually, you should check the number of Presented probes, instead
just the detection rate. For your case, it has more than ten thousand probes
are Present, which is reasonably good. You can lower the p-value threshold
to 0.05 to get more genes.


Pan


On 4/24/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 12
> Date: Thu, 24 Apr 2008 16:21:49 +1000
> From: "Yogi Sundaravadanam" <yogi.sundaravadanam at agrf.org.au>
> Subject: [BioC] Detection slot - Lumi
> To: bioconductor <bioconductor at stat.math.ethz.ch>
> Message-ID: <H000029400465e39.1209018106.mailmaster.agrf.org.au at MHS>
> Content-Type: text/plain
> 
> Hi All
> 
> For 46628 features (illumina Mouse chip), one of my sample has roughly
> about 22% of the genes that are detectable at a detection P value of 1%
> (according to the QC summary in lumi package).
> 
>  
> 
> I am not sure if this is considered BAD? I tried reading about this but
> don‚t seem to get anywhere. Any pointers will be of great help
> 
>  
> 
> Thanks heaps
> 
> Yogi 
>