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] <mailto:[email protected]>
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