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 > >
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