[BioC] simpleaffy QCstats and affyQAReport repost

[Crispin Miller]

Dear All,
I've added three functions to the devl version of simpleaffy (2.11.22).
These allow you to add (or change) the QC parameters for a chip if it's
not in simpleaffy. 

These are:

setAlpha(...)
setAllSpikeProbes(...)
and
setAllQCProbes(...)

For example:

> cdfname <- cleancdfname(cdfName(eset))
> setAlpha(cdfname,0.05,0.065)

Will add alpha1 and alpha2 values for the arraytype specified by cdfname
(in this case taken from an ExpressionSet object).

Similarly, setAllSpikeProbes() needs the probeset names for the four
BioB, BioC, BioD and CreX spikes, and setAllQCProbes(...) needs the 3',M
and 5' probesets for gapdh and beta-actin.

Thus: 

setAlpha("hgu133plus2cdf",0.05,0.065)
setAllQCProbes("hgu133plus2cdf",
 
"AFFX-HSAC07/X00351_3_at","AFFX-HSAC07/X00351_M_at","AFFX-HSAC07/X00351_
5_at", 
               "AFFX-HUMGAPDH/M33197_3_at","AFFX-HUMGAPDH/M33197_M_at",
"AFFX-HUMGAPDH/M33197_5_at")

setAllSpikeProbes("hgu133plus2cdf",
                  "AFFX-r2-Ec-bioB-3_at", "AFFX-r2-Ec-bioC-3_at", 
                  "AFFX-r2-Ec-bioD-3_at","AFFX-r2-P1-cre-3_at")

Would (if you needed to) set up the hgu133plus2 array.

Crispin
 
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