[BioC] Simpleaffy: how are 3/5 ratios calculated

[Yogi Sundaravadanam]

Dear Ganiraju,

Since the values stored in the QCStats object have been transformed using the base 2 logarithm ,they have to be transferred back to linear scale before calculation of the ratio. The 3'/5' ratios for the GAPDH gene can be displayed with the following code

(2^data at qc.probes[,4]) / (2^data at qc.probes[,6])
The corresponding values for the B-Actin gene:
(2^data at qc.probes[,1]) / (2^data at qc.probes[,3])

Is this what you are doing?

Cheers
Yogi


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-----Original Message-----
From: Ganiraju Manyam [mailto:ganican at gmail.com] 
Sent: Friday, September 26, 2008 1:12 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Simpleaffy: how are 3/5 ratios calculated

Hello,

I am currently looking at the simpleaffy package for affymetrix data QC.
I have a question regarding the 3'/5' ratio reported in the graph and by
the function "ratios"

This ratio is different from the ratio obtained by using the value reported
by the qcProbes() function and making the division "by hand".

Even I see negative ratios. Using the data from qcProbes(), i guess negative
ratios are not possible.

Can some expert elaberate the background process going on here?

Thanks for your time.

Ganiraju

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