Hi,
first of all, for this chip type you need to specify:
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
Moreover, you cannot use the custom CDF in the
GcRmaBackgroundCorrection step, and have to do the follow workaround
illustrated in the below example:
library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
dataSet <- "Affymetrix-Tissues";
chipType <- "MoEx-1_0-st-v1";
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Setup data set
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR1,A20080718,MR");
print(cdf);
csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType);
print(csR);
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# gcRMA-style background correction
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# Currently, you must use the standard CDF file.
cdf <- getCdf(csR);
cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE));
setCdf(csR, cdfS);
bc <- GcRmaBackgroundCorrection(csR, type="affinities");
print(bc);
csB <- process(bc, verbose=verbose);
print(csB);
# Now, use the custom CDF in what follows
setCdf(csB, cdf);
print(csB);
Yes, those last steps are rather confusing - we're working on updating
the code so you don't have to do that yourself.
FYI, the above solution/workaround was resolved in thread 'GCRMA
normalization with MoEx-1_0-st-v1' of March 24-April 8, 2010, cf.
http://goo.gl/cniq.
Hope this helps
/Henrik
On Fri, Sep 24, 2010 at 2:30 PM, Prithish Banerjee
<prithish.baner...@gmail.com> wrote:
> Hi All,
> I am trying to normalize a mouse exon array dataset using GCRMA
> normalization technique. I have exactly followed all the necessary steps for
> storing the dataset and the cdf file. the code and the output I am using are
> as follows:
>
> source("http://aroma-project.org/hbLite.R";);
>
> hbInstall("aroma.affymetrix")
>
> source("http://aroma-project.org/hbLite.R";);
>
> hbInstall("aroma.cn")
>
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>
> dataSet <- "Exon Data" [the path in the working directory is rawData/Exon
> Data/MoEx-1_0-st-v1/*.CEL files]
>
> chipType <- "MoEx-1_0-st-v1" [the path in the working directory is
> annotationData/chipTypes/MoEx-1_0-st-v1/MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf]
>
> cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
> [converted to binary using convertCdf command]
>
> print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/MoEx-1_0-st-v1
>
> Filename: MoEx-1_0-st-v1,coreR1,A20080718,MR.cdf
>
> Filesize: 30.53MB
>
> Chip type: MoEx-1_0-st-v1,coreR1,A20080718,MR
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 2560x2560
>
> Number of cells: 6553600
>
> Number of units: 17831
>
> Cells per unit: 367.54
>
> Number of QC units: 1
>
> csR <- AffymetrixCelSet$byName(dataSet, chipType=chipType)
>
> print(csR)
>
> AffymetrixCelSet:
>
> Name: Exon Data
>
> Tags:
>
> Path: rawData/Exon Data/MoEx-1_0-st-v1
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Number of arrays: 7
>
> Names: DK Litter D15 P1_(MoEx-1_0-st-v1), DK Litter D15
> P14_(MoEx-1_0-st-v1), ..., DK Litter D15 P6_(MoEx-1_0-st-v1)
>
> Time period: 2009-06-18 13:22:04 -- 2009-06-30 15:13:54
>
> Total file size: 440.55MB
>
> RAM: 0.01MB
>
> cdf <- getCdf(csR)
>
> cdfS <- AffymetrixCdfFile$byChipType(getChipType(cdf, fullname=FALSE))
>
> setCdf(csR, cdfS)
>
> bc <- GcRmaBackgroundCorrection(csR, type="affinities")
>
> print(bc)
>
> GcRmaBackgroundCorrection:
>
> Data set: Exon Data
>
> Input tags:
>
> User tags: *
>
> Asterisk ('*') tags: GRBC
>
> Output tags: GRBC
>
> Number of files: 7 (440.55MB)
>
> Platform: Affymetrix
>
> Chip type: MoEx-1_0-st-v1
>
> Algorithm parameters: (subsetToUpdate: NULL, typesToUpdate: chr "pm",
> indicesNegativeControl: NULL, affinities: NULL, type: chr "affinities",
> opticalAdjust: logi TRUE, gsbAdjust: logi TRUE, gsbParameters: NULL)
>
> Output path: probeData/Exon Data,GRBC/MoEx-1_0-st-v1
>
> Is done: FALSE
>
> RAM: 0.00MB
>
> csB <- process(bc, verbose=verbose)
>
> 20100923 13:24:12|Background correcting data set...
>
> 20100923 13:24:12| Computing probe affinities...
>
> 20100923 13:24:12| Computing GCRMA probe affinities for 1257006 units...
>
> 20100923 13:24:12| Identify PMs and MMs among the CDF cell indices...
>
> logi [1:5266159] TRUE TRUE TRUE TRUE TRUE TRUE ...
>
> Mode FALSE TRUE NA's
>
> logical 334476 4931683 0
>
> 20100923 13:25:57| MMs are defined as non-PMs
>
> 20100923 13:25:57| Number of PMs: 4931683
>
> 20100923 13:25:57| Number of MMs: 334476
>
> 20100923 13:25:57| Identify PMs and MMs among the CDF cell indices...done
>
> 20100923 13:25:57| Reading probe-sequence data...
>
> 20100923 13:25:57| Retrieving probe-sequence data...
>
> 20100923 13:25:57| Chip type (full): MoEx-1_0-st-v1
>
> 20100923 13:25:57| Locating probe-tab file...
>
> 20100923 13:25:57| Chip type: MoEx-1_0-st-v1
>
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.GcRmaBackgroundCorrection(bc, verbose = verbose)` = <environment>,
> :
>
>
>
> [2010-09-23 13:25:57] Exception: Found probe-tab file only by means of
> deprectated (v1) search rules:
>
> at throw(Exception(...))
>
> at throw.default("Found probe-tab file only by means of deprectated (v1
>
> at throw("Found probe-tab file only by means of deprectated (v1) search
>
> at method(static, ...)
>
> at AffymetrixProbeTabFile$findByChipType(chipType, what = what, ...)
>
> at method(static, ...)
>
> at AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose = les
>
> at getProbeSequenceData.AffymetrixCdfFile(this, safe = safe, verbose =
>
> at getProbeSequenceData(this, safe = safe, verbose = verbose)
>
> at computeAffinities.AffymetrixCdfFile(cdf, paths = probePath, ..., ver
>
> at computeAffinities(cdf, paths = probePath, ..., verbose = less(verbos
>
> at bgAdjustGcrma.AffymetrixCelSet(NA, path = "probeData/Exon Data,GRBC/
>
> at bgAdjustGcrma(NA, path = "probeData/Exon Data,GRBC/MoEx-1_0-st-v1",
>
> at do.call("bgAdjustGcrma", args = args)
>
> at process.GcRmaBackgroundCorrection(
>
> 20100923 13:25:57| Locating probe-tab file...done
>
> 20100923 13:25:57| Retrieving probe-sequence data...done
>
> 20100923 13:25:57| Reading probe-sequence data...done
>
> 20100923 13:25:57| Computing GCRMA probe affinities for 1257006
> units...done
>
> 20100923 13:25:57| Computing probe affinities...done
>
> 20100923 13:25:57|Background correcting data set...done
>
> Could anyone please enlighten me with the type of the error? I will be
> highly obliged if anyone please help me with this problem.
>
> Thank you.
>
> Prithish Banerjee.
>
>
>
> --
> 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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>
--
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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