Question: Converting makeProbePackage in AnnotationDbi to permit PM-only arrays
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8.2 years ago by
Ariel Grostern80 wrote:
Hi, I am attempting to adapt the makeProbePackage function in AnnotationDbi to permit me to make a probe package for my PM-only Affy array, so that I can then use altcdfenvs to re-annotate the probes. My probe sequence file is set up exactly as the normal tab-limited PM/MM file. >From examining the makeProbePackage.R file, it appears that there is only limited referral to MM probes, so I am eliminating them (see below). However, there is one section that I don't know what to do with: ## On most chips, PM and MM probe are next to each other on the chip, at same ## x coordinate and at adjacent y coordinates. Then, "sizex" is always the same, ## namely the size of the chip in x-direction. On some chips, there are few ## exceptions. tab = table(mm1-pm1) ## WHAT TO DO FOR THE ABOVE LINE? sizex = as.numeric(names(tab))[ max(tab)==tab ] can I replace the "tab" line with: tab=table(pm1) Thanks for any input, Ariel ## ---------------------------------------------------------------------- ## The table pt contains a probe to probe-set mapping (many-to-one). ## The CDF environment contains a probe-set to probe mapping (one-to- many). ## Here, we check whether they agree. ## In addition, it uses the information in the CDF to guess ## sizex, the size of the chip in x-direction. ## This is done using the fact that with current-day Affymetrix ## for each PM probe at (x,y) there is a MM probe at (x,y+1). ## (C) Laurent Gautier, Wolfgang Huber 2003 ## ---------------------------------------------------------------------- .lgExtraParanoia = function (pt, cdfname) { do.call(library, list(cdfname)) thecdf <- as.environment(paste("package", cdfname, sep=":"))[[cdfname]] ## Unroll CDF in order to invert the mapping from probe-set -> probe ## to probe -> probe-set. psnm1[i] is the probe set name for the i-th probe probesetnames = ls(thecdf) pm1 = unlist(lapply(probesetnames, function(ps) {thecdf[[ps]][,1]})) ## Crossed out the mm1 function ##mm1 = unlist(lapply(probesetnames, ## function(ps) {thecdf[[ps]][,2]})) psnm1 = unlist(lapply(probesetnames, function(ps) {rep(ps, nrow(thecdf[[ps]]))})) ## On most chips, PM and MM probe are next to each other on the chip, at same ## x coordinate and at adjacent y coordinates. Then, "sizex" is always the same, ## namely the size of the chip in x-direction. On some chips, there are few ## exceptions. ##tab = table(mm1-pm1) tab = table(pm1) ## WHAT TO DO FOR THE ABOVE LINE? sizex = as.numeric(names(tab))[ max(tab)==tab ] ## The probe indices according to pt pm2 = pt$y * sizex + pt$x + 1 ## Crossed out the mm2 function ## mm2 = (pt$y+1) * sizex + pt$x + 1 psnm2 = pt[["Probe.Set.Name"]] ## Check if the probe set names that are associated with each probe ## are the same in both CDF and pt ## z1 = z2 = rep(NA, max(pm1, mm1, pm2, mm2)) ## z1[pm1] = z1[mm1] = psnm1 ## z2[pm2] = z2[mm2] = psnm2 ## Remove mm1 and mm3 referals z1 = z2 = rep(NA, max(pm1, pm2)) z1[pm1] = psnm1 z2[pm2] = psnm2
cdf probe affy altcdfenvs • 546 views
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written 8.2 years ago by Ariel Grostern80
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