[BioC] QC questions

[Crispin Miller]

Dear Georg,

There's been a few questions about the QC stuff in simpleaffy - mainly
to do with finding QC data on different arrays. The way the package
works is that there are some tables containing the names of the QC
probes, alpha1 and alpha2 parameters, etc. that are array specific. The
error your getting is because I've not put zebrafish arrays into the
tables yet. I'll do this and let you know.

Cheers,
Crispin
-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Georg Otto
Sent: 11 October 2004 16:42
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] problems using cdfenv

Dear bioconductors,

i have a problem that presumably concerns my cdfenv installation.

I use the zebrafish affymetrix gene chip, and I tried simpleaffy to get
some quality control measures. Getting the expression measures with
mas5 seems to work fine, but

 > qc<-qc(x, x.mas5)

Gives me an error message:

Error in qc.affy(unnormalised, ...) : I'm sorry I do not know about chip
type: zebrafishcdf

I installed the zebrafishcdf from the bioconductor website but i still
get the same error. Then I made the cdf environment myself using the CDF
file from Affymetrix and makecdfenv. Unfortunately there is still the
same error.

Is there something that I missed?

Best regards,

Georg
 
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