[BioC] 3' 5' ratio
Crispin Miller
CMiller at PICR.man.ac.uk
Tue Oct 28 16:58:09 MET 2003
Sorry - a typo - a 3 crept in instead of a 5 - it should be 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_5_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);
}
> -----Original Message-----
> From: Crispin Miller
> Sent: 28 October 2003 15:39
> To: 'Sylvia Merk'
> Cc: Bioconductor (bioconductor at stat.math.ethz.ch)
> Subject: RE: [BioC] 3' 5' ratio
>
>
> 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
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo> /bioconductor
> >
>
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