[BioC] QC Parameter File error

[James W. MacDonald]

Hi Louisa,

Louisa A Rispoli/AS/EXP/UTIA wrote:
> Dear all,
> 
> Having an error message come up when trying to use qc on my bovine affy
> genechips
> 
> "Error in setQCEnvironment(cdfn) :
>   Could not find array definition file ' bovinecdf.qcdef '. Simpleaffy does
> not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters
> manually."
> 
> I doubled checked that I had uploaded the latest bovinecdf package (2.0.0
> versus 1.4.8 version)  but neither solves the issue. I know I can set the
> file myself using cdfName and cleancdfname but need to know where I go to
> doublecheck that I have the right values for the alphas and controls?

Not sure about the alphas - it seems like (0.05, 0.065) are common to 
use. For the controls, look at the last two pages of the simpleaffy 
vignette. You need the AFFX probeset IDs that correspond to these spike 
in and control probesets. You can look for them using e.g.,

prbs <- ls(bovinecdf)
affxprbs <- prbs[grep("AFFX", prbs)]

then look at affxprbs to see which ones correspond to what you see in 
the back of the simpleaffy vignette.

Next, see

http://article.gmane.org/gmane.science.biology.informatics.conductor/14298/match=qc+parameter

for how to get set up.

Best,

Jim


> 
> Any help would be apprecaited. I am new to this and still figuring it all
> out.
> 
> Thanks
> 
> Louisa Rispoli
> 
> 
> "If we knew what we were doing, it wouldn't be called Research." - Albert
> Einstein
> 
> _______________________________________________
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623