[BioC] question regarding qc function in simpleaffy package

[Groot, Philip de]

Hello James,
 
I am surprised to see that - apparently - simpleaffy detects that another chip is provided than returned via the 'annotation(raw.data)' function. Such a message would worry me indeed. Having said this: why would you want to perform QC utilizing the MBNI Custom CDF? The Custom CDF won't 'magically' improve bad quality arrays! In other words: performing QC utilizing the (default) Affymetrix CDF is just fine to assess thequality of your arrays.
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: James Anderson [mailto:janderson_net at yahoo.com]
Sent: Wed 31-3-2010 15:31
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] question regarding qc function in simpleaffy package



Hi,

I am trying to use the qc function in the simpleaffy package to generate those qc metrics for a bunch of cel files in U133A, but I need to use a different cdf file, not the Affy CDF.

Below is the code

library(simpleaffy)
cel.path <- "C:\Cel"
fn <- list.celfiles(cel.path, full.name = T)
raw.data <- ReadAffy(filenames = fn,cdfname = "hgu133ahsentrezg")  
x.mas5 <- call.exprs(raw.data,"mas5",sc = 100)
qcmas5 <- qc(raw.data,x.mas5)

Everything runs smoothly except the last line, it has the following warning message:

Warning message:
In qc.affy(unnormalised, ...) :
  CDF Environment name ' hgu133acdf ' does not match cdfname ' hgu133ahsentrezgcdf '

Is this problem negligible? or it is serious? I've looked into the qc function and it does not seem to have an argument that allows you to specify cdfname.

Thanks,

-James