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:





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

cdf <- AffymetrixCdfFile$byChipType(chipType,tags="coreR1,A20080718,MR")
[converted to binary using convertCdf command]



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)



Name: Exon Data


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")



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

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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