I actually solved this particular problem. I mixed up my cdf files somewhere along the line.
What I was trying to do was take the match scores from the bpmap file for the Mouse Promoter Tiling Array NCBIv35(mm7) since according to affymetrix the Mouse Promoter 1.0R array is a subset of that. So I had two separate sets of files. One from the bpmap provided by affy for the Mouse Promoter 1.0R array, and one from the larger tiling array. When I used the MAT cdfu I got that error. When I switched it over to the affy cdfu it was fine until farther down the line. I don't think my original idea will work though. It still breaks farther down the line at the MatSmoothing process. Eventually what I wound up doing was breaking up my data into the contrasts I wanted, exporting those as an affybatch, and running limma. That was all well and good, but when I get my results I don't get the affyid. Instead I get the genomic locations of the probe. Here's a sample of some top differentially expressed genes: ID logFC AveExpr t P.Value adj.P.Val B 23275 ;chrXFROM67710238TO67711428 6.68680949159341 6.52773618884153 130.653406044296 3.85160092999367e-23 9.17143213450092e-19 42.9794134788469 17860 ;chr6FROM83418224TO83422558 4.50358222665984 4.50858264809669 101.460787323948 1.35605633984657e-21 3.40179411765948e-18 39.8371438108809 7587 ;chr17FROM45304545TO45307125 4.7816883478266 4.73043521776862 100.563738822316 1.53666034926542e-21 3.40179411765948e-18 39.7220570955196 19337 ;chr7FROM7983765TO7992243 4.65337751179265 4.65059013150831 97.7668379856166 2.28578327915754e-21 3.40179411765948e-18 39.3546717418705 7421 ;chr17FROM34124518TO34132653 4.67620453488228 4.65734980713378 97.2182304190419 2.47422317349307e-21 3.40179411765948e-18 39.2810479487464 5042 ;chr14FROM53461958TO53468394 4.24264561081627 4.09812397107001 95.2364613673048 3.30636947315319e-21 3.40179411765948e-18 39.0106759253964 10221 ;chr1FROM34288931TO34297403 4.21179697960078 4.18961181796851 94.7083541900077 3.57557474020412e-21 3.40179411765948e-18 38.9374355054725 Do you know where I go from "23275 ;chrXFROM67710238TO67711428" to an affy_id I can then use to map to other databases? I've been looking at the documentation, but I'm stumped. On Jul 12, 4:49 am, Henrik Bengtsson <henrik.bengts...@aroma- project.org> wrote: > Hi. > > On Sun, Jul 10, 2011 at 10:03 PM, Jill <jillianrowe91...@gmail.com> wrote: > > Also, I noticed in the affxparser library the readCel has the value of > > NULL for indices. Could that be part of the problem? > > > readCel(filename, > > indices = NULL, > > readHeader = TRUE, > > readXY = FALSE, readIntensities = TRUE, > > readStdvs = FALSE, readPixels = FALSE, > > readOutliers = TRUE, readMasked = TRUE, > > No, I doubt that would be a problem. When 'indices' is NULL, it > defaults to reading everything. > > I order to troubleshoot this at all, would you mind making the > annotation files you've generated with bpmapCluster2Cdf() etc > available for download? > > /Henrik > > > > > On Jul 11, 7:54 am, Jill <jillianrowe91...@gmail.com> wrote: > >> Hello, > > >> I am trying to run a MAT normalization for some CEL data created from > >> Mouse Promoter 1.0R, and then to run a limma analysis. I have 8 levels > >> with 3 replicates of each level. > > >> ##Setup > >> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) > >> setwd("/home/jillian/microarray") > >> chipType <- "Mm_PromPR_v02" > >> cdf <- AffymetrixCdfFile$byChipType(chipType, verbose=verbose) > >> cs <- AffymetrixCelSet$byName("eman", cdf=cdf, verbose=verbose) > >> cs > >> # AffymetrixCelSet: > >> # Name: eman > >> # Tags: > >> # Path: rawData/eman/Mm_PromPR_v02 > >> # Platform: Affymetrix > >> # Chip type: Mm_PromPR_v02 > >> # Number of arrays: 24 > >> # Names: 0hDNA_1_WAS-KXX-110419-24-681_1, 0hDNA_2_WAS- > >> KXX-110419-24-681_2, 0hDNA_3_WAS-KXX-110419-24-681_3, ..., 6hK4_3_WAS- > >> KXX-110419-24-681_18 [24] > >> # Time period: 2011-04-20 07:32:01 -- 2011-04-20 16:34:21 > >> # Total file size: 1079.72MB > >> # RAM: 0.03MB > > >> ##MAT normalization > >> mn <- MatNormalization(cs) > >> csN <- process(mn, verbose=verbose, na.rm = TRUE) > >> csN > >> # AffymetrixCelSet: > >> # Name: eman > >> # Tags: MN,lm > >> # Path: probeData/eman,MN,lm/Mm_PromPR_v02 > >> # Platform: Affymetrix > >> # Chip type: Mm_PromPR_v02 > >> # Number of arrays: 24 > >> # Names: 0hDNA_1_WAS-KXX-110419-24-681_1, 0hDNA_2_WAS- > >> KXX-110419-24-681_2, 0hDNA_3_WAS-KXX-110419-24-681_3, ..., 6hK4_3_WAS- > >> KXX-110419-24-681_18 [24] > >> # Time period: 2011-07-10 11:37:50 -- 2011-07-10 11:51:29 > >> # Total file size: 1073.83MB > >> # RAM: 0.03MB > >> cdfU <- getUniqueCdf(cdf, verbose=verbose) > > >> csU <- convertToUnique(csN, verbose=verbose) > > >> When I run it I get this error: > >> 20110711 07:46:24| Converting CEL data from standard to unique CDF for > >> sample #1 (0hDNA_1_WAS-KXX-110419-24-681_1) of 24... > >> 20110711 07:46:24| Reading intensity values according to standard > >> CDF... > >> Error in readCel(filename, indices = indices, readHeader = FALSE, > >> readOutliers = FALSE, : > >> Argument 'indices' contains an element out of range. > > >> Also, if I run the csN <- process(mn, verbose=verbose, na.rm = TRUE) > >> without the na.rm=TRUE argument I get an error that there are NaN > >> values. > > >> I created the cdf file from the bpmap file the Liu Lab MAT provides > >> using the bpmapCluster2Cdf function. > > >> Looking through the group I saw someone else had the same problem, but > >> not how/if they solved it. > > >> Thanks! > > > -- > > 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 with websitehttp://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/ -- 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. 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