Hi Sebastien. Have a look at:
http://thread.gmane.org/gmane.science.biology.informatics.conductor/19591/ If you want these probesets, you might consider creating the CDF directly from a pdInfoBuilder package (which works directly from the PGF/CLF files from Affy), as described at: http://groups.google.com/group/aroma-affymetrix/web/creating-cdf-files-from-r-packages-environments Hope that helps. Mark On 11/02/2009, at 10:32 AM, Sebastien Gerega wrote: > > Hi, > I have come across some missing probes in the mogene10st.db package. I > am analysing my data using the aroma package and have included some of > my code: > > ces = getChipEffectSet(plm) > gExprs = extractDataFrame(ces, units=NULL, addNames=TRUE) > affyIDs = gExprs$unitName > > affyIDs[which(affyIDs %in% > names(unlist(as.list(mogene10stENTREZID))) == > FALSE)] > [1] "10344715" "10346139" "10348945" "10351859" "10361914" "10363331" > "10364435" "10372094" "10375121" > [10] "10388263" "10388269" "10393404" "10394238" "10396419" "10398315" > "10401420" "10406248" "10408136" > [19] "10408144" "10408900" "10409545" "10412699" "10418129" "10422509" > "10424416" "10427993" "10428439" > [28] "10433478" "10436198" "10439287" "10439409" "10439974" "10442153" > "10442256" "10445378" "10449547" > [37] "10450920" "10453715" "10457583" "10457778" "10458958" "10459467" > "10461790" "10462311" "10467838" > [46] "10482137" "10484695" "10485716" "10490984" "10495594" "10496888" > "10498497" "10502199" "10514325" > [55] "10514327" "10514329" "10514331" "10521698" "10527099" "10528157" > "10528159" "10528172" "10529815" > [64] "10530140" "10531631" "10535467" "10539979" "10540931" "10541349" > "10544538" "10546227" "10548697" > [73] "10550167" "10553786" "10553811" "10559498" "10571382" "10579607" > "10579763" "10583199" "10584393" > [82] "10591182" "10591184" "10595787" "10608198" "10608200" > > Are people aware of these missing probes? I have not been able to find > any documentation about the issue. Should I send this to the BioC > mailing list instead? > thanks for your help, > Sebastien > > > ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
