Hi All, Why don't the numbers from summary(hgu95av2probe):199084 and length(pbn): 201800 don't match?!! There are more sequences than probe names?! I am including code snippet. Thanks, Hrishi data(hgu95av2probe) > summary(hgu95av2probe) sequence x y Probe.Set.Name Length:199084 Min. : 1.0 Min. : 1.0 Length:199084 Class :AsIs 1st Qu.:161.0 1st Qu.:161.0 Class :AsIs Mode :character Median :319.0 Median :319.0 Mode :character Mean :319.1 Mean :319.8 3rd Qu.:478.0 3rd Qu.:479.0 Max. :638.0 Max. :637.0 Probe.Interrogation.Position Target.Strandedness Min. : 14 Antisense:198784 1st Qu.: 865 Sense : 300 Median : 1649 Mean : 2132 3rd Qu.: 2856 Max. :20813 > pbn<-probeNames(M[,1]) > length(pbn) [1] 201800

Hi Hrishikesh, > Why don't the numbers from > summary(hgu95av2probe):199084 > and length(pbn): 201800 don't match?!! > There are more sequences than probe names?! 199084 is less than 201800 hence there are fewer sequences than probe names. The data file from Affymetrix from which the hgu95av2probe table was obtained (1:1 without any additions/omissions) contains that number of probes. The remainder may be control or 'empty' probes. Hope this helps, Wolfgang > > I am including code snippet. > > Thanks, > Hrishi > > data(hgu95av2probe) > >>summary(hgu95av2probe) > > sequence x y > Probe.Set.Name > Length:199084 Min. : 1.0 Min. : 1.0 > Length:199084 > Class :AsIs 1st Qu.:161.0 1st Qu.:161.0 > Class :AsIs > Mode :character Median :319.0 Median :319.0 > Mode :character > Mean :319.1 Mean :319.8 > > 3rd Qu.:478.0 3rd Qu.:479.0 > > Max. :638.0 Max. :637.0 > > Probe.Interrogation.Position Target.Strandedness > Min. : 14 Antisense:198784 > 1st Qu.: 865 Sense : 300 > Median : 1649 > Mean : 2132 > 3rd Qu.: 2856 > Max. :20813 > > >>pbn<-probeNames(M[,1]) >>length(pbn) > > [1] 201800 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Best regards Wolfgang ------------------------------------- Wolfgang Huber European Bioinformatics Institute European Molecular Biology Laboratory Cambridge CB10 1SD England Phone: +44 1223 494642 Fax: +44 1223 494486 Http: www.ebi.ac.uk/huber

Dear Sir, Thanks for the prompt help.One more question: Does the probe BioC package provides probe sequences for "quality control" probes like bioB, bioC,.. etc? I downloaded the hgu_95av2 probe package and looked in hgu95av2probe.rda and i couldn't find any qualtiy control probes (part of .rda was in binary!!). Thanks, Hrishi

Hrishikesh Deshmukh <d_hrishikesh@yahoo.com> writes: > Dear Sir, > > Thanks for the prompt help.One more question: > Does the probe BioC package provides probe sequences > for "quality control" probes like bioB, bioC,.. etc? > I downloaded the hgu_95av2 probe package and looked in > hgu95av2probe.rda and i couldn't find any qualtiy > control probes (part of .rda was in binary!!). When you say, "looked in hgu95av2probe.rda", what did you do? The .rda files are binary files. In general, you load them into an R session to examine the R objects they contain using the load function. + seth