Hi, sorry, there is currently nothing in aroma.affymetrix for calling probes present/absent. For questions on affy::mas5calls(), check with the Bioconductor mailing list.
Cheers, Henrik On Tue, Sep 25, 2012 at 4:05 PM, Heather Wick <heather.c.w...@gmail.com> wrote: > I would like to look at present/absent calls and the associated p-values for > a set of MoGene ST arrays I'm working on. I normalized the chips using the > Aroma vignette, but there are no instructions there for P/M/A calls. > Normally, I work with Hgu133plus2 arrays, so my instinct was to try reading > the cel files in with ReadAffy and then using mas5calls to extract this > data. However, I got this error: >> data.mas5calls=mas5calls(CelData) > Getting probe level data... > Computing p-values > Error in FUN(1:11[[1L]], ...) : > NA/NaN/Inf in foreign function call (arg 2) > > I'm sure there must be a way of getting present/absent calls/pvalues with ST > arrays, can someone point me in the right direction? > > I was also disappointed that I could not get percent present, average > background, or scale factor using qc on these chips; is there an equivalent > function for ST arrays? > > I cannot seem to find any information about this on the Aroma website or > searching through the forums. I greatly appreciate any advice you can offer. > ~ Heather Wick > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the latest > version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/