Edit:
Never mind. I had missed the calls to:
computeAffinities(cdfS, verbose=-8)
getAromaCellSequenceFile(cdfS)
so, after downloading the ACS file and running the above line, now gcRMA
appears to be working fine.
######### updated code sequence ##############
library('aroma.affymetrix')
dataSetName <- "GSE41055"
chipType <- "HuEx-1_0-st-v2"
cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2,fullR3,A20071112,EP",
verbose=-6)
cdf
csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf, verbose=-6)
csR
## need original CDF to do gcRMA (ie, not fullR3)
cdfS <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2", verbose=-8)
computeAffinities(cdfS, verbose=-8)
getAromaCellSequenceFile(cdfS) ## need to have ACS file for this piece
setCdf(csR, cdfS)
bcGC <- GcRmaBackgroundCorrection(csR, type="affinities")
csNgc <- process(bcGC, verbose=-8)
########################################################
Thanks, and sorry to bother--
Tim
On Thursday, June 4, 2015 at 11:38:19 PM UTC-7, Tim Sweeney wrote:
>
> Hello,
>
> I am having trouble getting gcRMA to work with a human exon array. I know
> this has been addressed before, eg:
> https://groups.google.com/forum/#!msg/aroma-affymetrix/QD6o-3XiifM/e8-5OaQ44qgJ,
>
> but my issue is slightly different. I used the code presented in that
> thread but got the following error from the GcRmaBackgroundCorrection()
> call:
>
> "Error: Did not find a probe-tab file even by means of deprectated (v1)
> search rules. Either way, such files are no longer supported."
>
> See code, error, and systemInfo() below.
>
> Note: This was run once with the custom (fullR3) cdf followed by Rma
> (instead of GCRma). In that instance, the code ran error-free.
>
> Many thanks,
>
> Tim Sweeney
>
>
> ############### code run: #######################
>
> library('aroma.affymetrix')
>
> dataSetName <- "GSE41055"
> chipType <- "HuEx-1_0-st-v2"
>
> cdf <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2,fullR3,A20071112,EP",
> verbose=-6)
> cdf
>
> csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf, verbose=-6)
> csR
>
>
> ## need original CDF to do gcRMA (ie, not fullR3)
> cdfS <- AffymetrixCdfFile$byChipType("HuEx-1_0-st-v2", verbose=-6)
> cdfS
> setCdf(csR, cdfS)
> csR
> bcGC <- GcRmaBackgroundCorrection(csR, type="affinities")
> csNgc <- process(bcGC, verbose=-8)
>
> ############### output from final line: #####################
>
> Background correcting data set...
> Computing probe affinities (independent of data)...
> Computing GCRMA probe affinities...
> Chip type: HuEx-1_0-st-v2
> Number of units: 1432154
> Locating the cell sequence annotation data file...
> Locating the cell sequence annotation data file...done
> Computing GCRMA probe affinities...done
> Computing GCRMA probe affinities...
> Number of units: 1432154
> Identify PMs and MMs among the CDF cell indices...
> logi [1:5518308] TRUE TRUE TRUE TRUE TRUE TRUE ...
> Mode FALSE TRUE NA's
> logical 73224 5445084 0
> MMs are defined as non-PMs
> Number of PMs: 5445084
> Number of MMs: 73224
> Identify PMs and MMs among the CDF cell indices...done
> Reading probe-sequence data...
> Retrieving probe-sequence data...
> Chip type (full): HuEx-1_0-st-v2
> Locating probe-tab file...
> Chip type: HuEx-1_0-st-v2
> [2015-06-04 23:13:00] Exception: Did not find a probe-tab file even by
> means of deprectated (v1) search rules. Either way, such files are no
> longer supported.
>
> at #14. findByChipType.AffymetrixProbeTabFile(static, ...)
> - findByChipType.AffymetrixProbeTabFile() is in environment
> 'aroma.affymetrix'
>
> at #13. findByChipType(static, ...)
> - findByChipType() is in environment 'aroma.core'
> - originating from '<text>'
>
> at #12. AffymetrixProbeTabFile$findByChipType(chipType, what = what,
> ...)
> - AffymetrixProbeTabFile$findByChipType() is local of the
> calling function
>
> at #11. byChipType.AffymetrixProbeTabFile(static, ...)
> - byChipType.AffymetrixProbeTabFile() is in environment
> 'aroma.affymetrix'
>
> at #10. byChipType(static, ...)
> - byChipType() is in environment 'aroma.core'
> - originating from '<text>'
>
> at #09. AffymetrixProbeTabFile$byChipType(chipType = chipType, verbose =
> less(verbose,
> 100))
> - AffymetrixProbeTabFile$byChipType() is local of the calling
> function
>
> at #08. getProbeSequenceData.AffymetrixCdfFile(this, safe = safe,
> verbose = verbose)
> - getProbeSequenceData.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #07. getProbeSequenceData(this, safe = safe, verbose = verbose)
> - getProbeSequenceData() is in environment 'aroma.affymetrix'
>
> at #06. computeAffinities.AffymetrixCdfFile(cdf, ..., verbose =
> less(verbose))
> - computeAffinities.AffymetrixCdfFile() is in environment
> 'aroma.affymetrix'
>
> at #05. computeAffinities(cdf, ..., verbose = less(verbose))
> - computeAffinities() is in environment 'aroma.affymetrix'
>
> at #04. calculateAffinities.GcRmaBackgroundCorrection(this, verbose =
> less(verbose))
> - calculateAffinities.GcRmaBackgroundCorrection() is in
> environment 'aroma.affymetrix'
>
> at #03. calculateAffinities(this, verbose = less(verbose))
> - calculateAffinities() is in environment 'aroma.affymetrix'
>
> at #02. process.GcRmaBackgroundCorrection(bcGC, verbose = -8)
> - process.GcRmaBackgroundCorrection() is in environment
> 'aroma.affymetrix'
>
> at #01. process(bcGC, verbose = -8)
> - process() is in environment 'aroma.core'
>
> Show Traceback
>
> Rerun with Debug
> Error: Did not find a probe-tab file even by means of deprectated (v1)
> search rules. Either way, such files are no longer supported.
> Locating probe-tab file...done
> Retrieving probe-sequence data...done
> Reading probe-sequence data...done
> Computing GCRMA probe affinities...done
> Computing probe affinities (independent of data)...done
> Background correcting data set...done
>
> ##################### sessionInfo()
> ##############################################
>
> R version 3.1.1 (2014-07-10)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] preprocessCore_1.24.0 aroma.light_1.32.0 matrixStats_0.14.0
> aroma.affymetrix_2.13.2 aroma.core_2.13.1
> [6] R.devices_2.13.0 R.filesets_2.7.2 R.utils_2.1.0
> R.oo_1.19.0 affxparser_1.34.2
> [11] R.methodsS3_1.7.0
>
> loaded via a namespace (and not attached):
> [1] aroma.apd_0.6.0 base64enc_0.1-2 Cairo_1.5-6 digest_0.6.8
> DNAcopy_1.36.0 PSCBS_0.44.0 R.cache_0.10.0
> [8] R.huge_0.9.0 R.rsp_0.20.0 tools_3.1.1
>
--
--
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