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 website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/