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!
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