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.
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