[BioC] Summary Statistics

[Michael Newton]

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
> >
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>
>
> --
> 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
>
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