Dear all, I have 25 cel files from Affymetrix U133AAofAv2 platform. I need to quantify the data using fRMA. Since there is no available vector package for this platform, I have to construct one using frma Tools. Here is my code and the "missing value" problem when generating this vector. Any help will be highly appreciated. Thank you very much. > u133aaofav2frmavecs=makeVectorsAffyBatch(cel.files, 1:25, file.dir=celpath) Read in: .... ....... Data loaded Background Corrected Normalized Beginning Probe Effect Calculation ... Finished probeset: 1000 Finished probeset: 2000 Finished probeset: 3000 Finished probeset: 4000 Finished probeset: 5000 Finished probeset: 6000 Finished probeset: 7000 Finished probeset: 8000 Finished probeset: 9000 Finished probeset: 10000 Finished probeset: 11000 Finished probeset: 12000 Finished probeset: 13000 Finished probeset: 14000 Finished probeset: 15000 Finished probeset: 16000 Finished probeset: 17000 Finished probeset: 18000 Finished probeset: 19000 Finished probeset: 20000 Finished probeset: 21000 Finished probeset: 22000 Probe Effects Calculated Probe Variances Calculated Probe Set SDs Calculated Beginning Median SE Calculation ... Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed Best, Ying [[alternative HTML version deleted]]

In your makeVectors call, it appears you are saying you only have one array per batch and only 25 arrays total. I believe this is what is producing the error. You need multiple arrays per batch to create frmavecs. And you should probably use more than 25 arrays to create the frmavecs. Best, Matt On Nov 10, 2011 9:10 AM, "Wang,Ying" <ywang31@mdanderson.org> wrote: > Dear all, > > I have 25 cel files from Affymetrix U133AAofAv2 platform. I need to > quantify the data using fRMA. Since there is no available vector package > for this platform, I have to construct one using frma Tools. Here is my > code and the "missing value" problem when generating this vector. Any help > will be highly appreciated. Thank you very much. > > > u133aaofav2frmavecs=makeVectorsAffyBatch(cel.files, 1:25, > file.dir=celpath) > Read in: .... > ....... > > Data loaded > > Background Corrected > > Normalized > > Beginning Probe Effect Calculation ... > > Finished probeset: 1000 > > Finished probeset: 2000 > > Finished probeset: 3000 > > Finished probeset: 4000 > > Finished probeset: 5000 > > Finished probeset: 6000 > > Finished probeset: 7000 > > Finished probeset: 8000 > > Finished probeset: 9000 > > Finished probeset: 10000 > > Finished probeset: 11000 > > Finished probeset: 12000 > > Finished probeset: 13000 > > Finished probeset: 14000 > > Finished probeset: 15000 > Finished probeset: 16000 > > Finished probeset: 17000 > > Finished probeset: 18000 > > Finished probeset: 19000 > > Finished probeset: 20000 > > Finished probeset: 21000 > > Finished probeset: 22000 > > Probe Effects Calculated > > Probe Variances Calculated > > Probe Set SDs Calculated > > Beginning Median SE Calculation ... > > Error in if (any(w < 0)) { : missing value where TRUE/FALSE needed > > > Best, > > Ying > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]