Hi All,
Is is possible to do summary statistics on individual
CEL files?! How does one accept or reject a CEL file
(from replicates) for further study?
Thanks,
Hrishi
Hrishikesh Deshmukh wrote:
> Hi All,
>
> Is is possible to do summary statistics on individual
> CEL files?! How does one accept or reject a CEL file
> (from replicates) for further study?
I use two criteria for rejecting celfiles. First, I look at the plot
of
the PM distributions. If you are using RMA, any chip that is 'too far'
from the others in a set will usually not work well. Unfortunately, it
is difficult to quantify what 'too far' really is. If there appears to
be an outlier, I follow up with a look at the residuals from the
medianpolish fit (using rmaPLM() and image(Pset, type = "resid") from
the affyPLM package). Again, this is an eyeballometric call on my
part.
If the possible outlier appears to have much larger outliers on the
residual plot, I either reject it or we re-fragment and re-hyb the
sample.
HTH,
Jim
>
> Thanks,
> Hrishi
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
Is eyeballometrics part of eyeballomics?
On Fri, 11 Mar 2005, James W. MacDonald wrote:
> Hrishikesh Deshmukh wrote:
> > Hi All,
> >
> > Is is possible to do summary statistics on individual
> > CEL files?! How does one accept or reject a CEL file
> > (from replicates) for further study?
>
> I use two criteria for rejecting celfiles. First, I look at the plot
of
> the PM distributions. If you are using RMA, any chip that is 'too
far'
> from the others in a set will usually not work well. Unfortunately,
it
> is difficult to quantify what 'too far' really is. If there appears
to
> be an outlier, I follow up with a look at the residuals from the
> medianpolish fit (using rmaPLM() and image(Pset, type = "resid")
from
> the affyPLM package). Again, this is an eyeballometric call on my
part.
> If the possible outlier appears to have much larger outliers on the
> residual plot, I either reject it or we re-fragment and re-hyb the
sample.
>
> HTH,
>
> Jim
>
>
> >
> > Thanks,
> > Hrishi
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
> --
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
Michael Newton wrote:
> Is eyeballometrics part of eyeballomics?
>
Actually, yes it is. It is almost as cutting edge as kinomics (which
recently surpassed proteomics on the uber-cool buzzword scale) ;-D
A highly recommended field for all up-and-coming biostat PhD
candidates.
--
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
