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.
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