[BioC] Variability Plot For Toray Microarray Data

[Steve Lianoglou]

Hi Peverall,

On Mon, Jan 28, 2013 at 7:34 PM, Peverall Dubois
<peveralldubois at gmail.com> wrote:
> Is there any package that allow you to perform "MA plot" like graph
> for Toray microarray data?
>
>
> Unlike Affymetrix CEL file which contain 2 values (R and G),
> Torray raw data only contain 1 value.

Actually, affy chips are not two color arrays (R and G, aka "red" and
"green"), they are also "1 color" arrays like I guess the Toray is
(disclaimer: this is the first time of heard of a toray, so I have no
idea what makes a torray a toray).

Are the two values you are referring to on an affy chip the "perfect
match" and "mismatch" probes, maybe? If so, you should know that most
people don't really use the info from the mismatch probes these days
... RMA, for instance, only uses information from perfect match
probes.

> MA-plot is Affymetrix specific which usually available for in  (limma)
> package.

The two values that are averaged and "log-fold-changed" in an MA plot
for affy arrays array always from datasets that have 2+ arrays. These
statistics are either generated across replicates (so 1 array vs
another), or sometimes 1 array vs a pseudo-array, which might be the
mean expression of the probes across your samples.

All this having been said, I have no idea if anyone has rigged up
support for toray microarrays in bioconductor-land.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact