[BioC] 3' 5' ratio

[Crispin Miller]

Hi,
try this:

qc.ratios <-function(x,logged=T) {
  x <- exprs(x);
  if(!logged) { x <- log2(x); }
  rats <- 2^cbind((x["AFFX-HUMGAPDH/M33197_3_at",] -
x["AFFX-HUMGAPDH/M33197_5_at",]),
                  (x["AFFX-HUMGAPDH/M33197_3_at",] -
x["AFFX-HUMGAPDH/M33197_M_at",]),
                  (x["AFFX-HSAC07/X00351_3_at",]   -
x["AFFX-HSAC07/X00351_3_at",]),
                  (x["AFFX-HSAC07/X00351_3_at",]   -
x["AFFX-HSAC07/X00351_M_at",]));
  colnames(rats) <-
c("GAPDH.3'/5'","GAPDH.3'/M","beta.actin.3'/5'","beta.actin.3'/M");
  return(rats);
}

Where x is an AffyBatch object and the data has been normalised using
the mas5 algorithm... And logged says whether the expression levels are
log2() or not... 

It gives you 3'/5' ratios and  also 3'/mid ratios for GAPDH and
beta-actin... It should work - I've checked it for one (hgu133a) array
;-)

Cheers,
Crispin



> -----Original Message-----
> From: Sylvia Merk [mailto:merk at ibe.med.uni-muenchen.de] 
> Sent: 28 October 2003 14:10
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] 3' 5' ratio
> 
> 
> Hi all,
> 
> I have cel-files from Affymetrix U133a+b chips and I wanted 
> to do some 
> quality control - so I read in the cel-files with the 
> affy-package  and 
> got an affybatch-object.
> Then I had a look at the RNA degradation plots. I know that 
> Microarray 
> suite performs 3'/5'-ratios as a quality check. My problem 
> is: I've only 
> got the cel-files - there is no other information from 
> Microarray suite 
> available. So my question is: is it possible to calculate  
> 3'/5'-ratios 
> out of the cel-file?
> Thank you in advance for your help.
> 
> Many greetings
> Sylvia
> 
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>
 
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