Hi Willem, It looks like you have Ensembl exon IDs if you remove the "_at" from ENSMUSE00000097912_at. You could use those Ensembl exon IDs to retrieve gene information from Ensembl through biomaRt.
Let me know if you need more help, Steffen On Thu, Nov 10, 2011 at 3:08 PM, Arek Kasprzyk <[email protected]>wrote: > Hi Willen, > you need a biomaRt specialist Steffen here (cc'ed on this email) > > a > > On Thu, Nov 10, 2011 at 6:45 AM, Talloen, Willem [JRDBE] < > [email protected]> wrote: > >> Hi all,**** >> >> ** ** >> >> I would like to link probes to exons as defined in Ensemble. The problem >> I face is that I cannot find probe IDs in Ensemble mapping.**** >> >> Could anyone help me with this? Probably biomaRt is a logical approach, >> but I cannot find it. I’m using alternative cdf from >> Brainarray<http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.0.0/entrezg.asp> >> .**** >> >> ** ** >> >> I tried via xy coordinates (see below), but there is quite some >> redundancy and it is not comprehensive…**** >> >> ** ** >> >> To make it more specific, below chunks of code that I’m currently using.* >> *** >> >> ** ** >> >> Thanks in advance!**** >> >> Willem**** >> >> ** ** >> >> ** ** >> >> # create probe intensity matrix for each probeset**** >> >> *for* *(*i *in* 1:length*(*gNames*))* *{***** >> >> myProbeSet *<-* gNames*[*i*]***** >> >> myPmindex *<-* unlist*(*pmindex*(*dataPreprocessed, myProbeSet*))** >> *** >> >> myDat *<-* intensity*(*dataPreprocessed*)**[*myPmindex, *]***** >> >> main = fProbeSet*)***** >> >> *}***** >> >> > head(myDat[,1:5])**** >> >> 2720.CEL 2724.CEL 2725.CEL 2727.CEL 2728.CEL**** >> >> 442478 2335.2318 943.1485 2239.6485 2250.0652 2247.3568**** >> >> 975758 2695.0235 1232.8152 2923.0652 2794.6485 2889.9402**** >> >> 211794 924.3985 383.6485 856.5652 942.0652 803.8152**** >> >> 388714 1377.1485 764.0652 1404.8568 1622.5652 1447.1485**** >> >> 137675 4211.3152 2051.3985 4294.8985 4459.4818 3699.2318**** >> >> 985031 3602.1485 1634.2318 3607.2735 3501.6068 3442.6485**** >> >> ** ** >> >> ** ** >> >> ** ** >> >> # load exon information**** >> >> ensMap *<-* read.delim*(*'../Mouse4302_Mm_ENSE_mapping.txt', sep = '\t'*) >> ***** >> >> > head(ensMap)**** >> >> Probe.Set.Name Chr Chr.Strand Chr.From Probe.X Probe.Y**** >> >> 1 ENSMUSE00000097912_at 10 - 6791726 451 421**** >> >> 2 ENSMUSE00000097912_at 10 - 6791765 724 625**** >> >> 3 ENSMUSE00000097912_at 10 - 6791790 613 565**** >> >> 4 ENSMUSE00000097912_at 10 - 6791850 147 367**** >> >> 5 ENSMUSE00000097912_at 10 - 6791866 790 251**** >> >> 6 ENSMUSE00000097912_at 10 - 6791883 405 115**** >> >> Affy.Probe.Set.Name**** >> >> 1 1451547_at**** >> >> 2 1451547_at**** >> >> 3 1451547_at**** >> >> 4 1451547_at**** >> >> 5 1451547_at**** >> >> 6 1451547_at**** >> >> ** ** >> >> # link via xy coordinates**** >> >> coord *<-* paste*(*ensMap*$*Probe.X, ensMap*$*Probe.Y, sep = '.'*)***** >> >> ** ** >> >> > i2xy(as.numeric(rownames(myDat)))**** >> >> x y**** >> >> [1,] 595 441**** >> >> [2,] 811 973**** >> >> [3,] 371 211**** >> >> [4,] 939 387**** >> >> Willem Talloen**** >> >> Janssen Pharmaceutica**** >> >> Biostatistics and Programming GDO CoE **** >> >> Turnhoutseweg 30, box 270**** >> >> 2340 Beerse 1**** >> >> Belgium**** >> >> Phone +32(0)14603434 Fax +32(0)14605802**** >> >> [email protected] <[email protected]>**** >> >> ** ** >> >> [image: Janssen_Hor_RGB]**** >> >> ** ** >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users >> >> >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
