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!
>
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