Dear BioC, Has any one got error in mas5calls(AffyBatchData) for Hu6800 arrays? I get below error: MASoutput <- mas5calls(AffyBatchData) Getting probe level data... Computing p-values Making P/M/A Calls Error in if (y < alpha1) { : missing value where TRUE/FALSE needed How can I resolve this error? Thank you in advance, Saurin

Hi Saurin, the Hu6800 cdf environment doesn't have a stored alpha1 and alpha2 value. Try the command $> MASoutput <- mas5calls(AffyBatchData,alpha1=0.05,alpha2=0.065) if you would like to use an alpha1 value of 0.05 and alpha2 of 0.065 for example. This should work, have a look at the help page of mas5calls. Unfortunately this solution doesn't work with the "pairwise.comparison"-method because that one doesn't accept a manual definition of the alpha values. Maybe somebody else has got an idea how to work around the problem with that function? Just as a remark: $> getAlpha1("hgu133plus2cdf") returns the current alpha1 value stored in the hgu133plus2cdf and is equal to $> get("alpha", envir = .qcEnv)["hgu133plus2cdf", "alpha1"] The following command displays both alpha values for all registred cdf environments providing them: $> get("alpha", envir = .qcEnv) Maybe there is some way to extend this table manually by desired entries or even update the goal cdf environment file permanent. But currently I can't tell how... regards, Benjamin > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Saurin D. > Jani > Sent: 17 January 2006 16:15 > To: bioconductor > Subject: [BioC] Error mas5calls(AffyBatchData) for Hu6800 arrays, - > help, > > > Dear BioC, > > Has any one got error in mas5calls(AffyBatchData) for Hu6800 arrays? > > I get below error: > > MASoutput <- mas5calls(AffyBatchData) > Getting probe level data... > Computing p-values > Making P/M/A Calls > Error in if (y < alpha1) { : missing value where TRUE/FALSE needed > > How can I resolve this error? > > Thank you in advance, > Saurin > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >