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,
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!
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