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. MA-plot is Affymetrix specific which usually available for in (limma) package. P. Dubois [[alternative HTML version deleted]]

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