Hi. Your versions of aroma.affymetrix and other packages are too old.
Please update. /Henrik
On Sun, Nov 30, 2008 at 11:46 PM, [EMAIL PROTECTED]
<[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> I do paired copy number analysis with code previous working well
> (with old version), this time it stopped in the PCR fragment length
> normalization step for some reason.
> Please help me with it, thanks.
>
> Yue
>
> -------My code-----------------
> setwd("//depts/CompDisc/yuehu/Cancerprofiling/workfolder")
> log <- Arguments$getVerbose(-4);
> timestampOn(log);
> dataSetName <- "Venkat2";
> pairs <- matrix(c(
> "1070a.CEL", "1070b.CEL", "2657a.CEL", "2657b.CEL", "3981a.CEL",
> "3981b.CEL",
> "4121a.CEL", "4121b.CEL", "5419a.CEL", "5419b.CEL", "5798a.CEL",
> "5798b.CEL",
> "6958a.CEL", "6958b.CEL", "8086a.CEL", "8086b.CEL"
> ), ncol=2, byrow=TRUE);
> colnames(pairs) <- c("Norm", "Tumor");
> library(aroma.affymetrix)
> verbose <- Arguments$getVerbose(-8)
> timestampOn(verbose)
> csRawList <- list();
> cdf <- AffymetrixCdfFile$fromChipType("GenomeWideSNP_6", tags="Full");
> cs <- AffymetrixCelSet$fromName("Venkat2", cdf=cdf)
> print(cs);
> csRawList[["GenomeWideSNP_6"]] <- cs;
>
> csAccList <- list();
>
> cs <- csRawList[["GenomeWideSNP_6"]];
> acc <- AllelicCrosstalkCalibration(cs);
> print(acc);
> csAcc <- process(acc, verbose=log);
> csAccList[["GenomeWideSNP_6"]] <- csAcc;
>
> cesList <- list();
>
> cs <- csAccList[["GenomeWideSNP_6"]];
> plm <- RmaCnPlm(cs, mergeStrands=TRUE, combineAlleles=TRUE, shift=
> +300);
> print(plm);
> fit(plm, verbose=log);
> ces <- getChipEffectSet(plm);
> cesList[["GenomeWideSNP_6"]] <- ces;
>
> cesFlnList <- list();
>
> ces <- cesList[["GenomeWideSNP_6"]];
> fln <- FragmentLengthNormalization(ces);
> print(fln);
> cesFln <- process(fln, verbose=verbose);
> cesFlnList[["GenomeWideSNP_6"]] <- cesFln;
>
> -------------Error message--------------
>> print(fln);
> FragmentLengthNormalization:
> Data set: Venkat2
> Input tags: ACC,ra,-XY,RMA,+300,A+B
> Output tags: ACC,ra,-XY,RMA,+300,A+B,FLN,-XY
> Number of arrays: 16 (431.19MB)
> Chip type: GenomeWideSNP_6,Full,monocell
> Algorithm parameters: (subsetToFit: chr "-XY", .targetFunctions:
> NULL, : num 0)
> Output path: plmData/Venkat2,ACC,ra,-XY,RMA,+300,A+B,FLN,-XY/
> GenomeWideSNP_6
> Is done: FALSE
> RAM: 0.00MB
>> cesFln <- process(fln, verbose=verbose);
> 20081130 22:53:17|Normalizing set for PCR fragment-length effects...
> 20081130 22:53:17| Identifying SNP and CN units...
> 20081130 22:53:17| Reading types for *all* units...
> 20081130 22:55:48| Reading types for *all* units...done
> 20081130 22:55:49| subsetToUpdate:
> int [1:1880794] 622 623 624 625 626 627 628 629 630 631 ...
> 20081130 22:55:49| Identifying SNP and CN units...done
> 20081130 22:55:49| Retrieving SNP information annotations...
> Error in footer$chipType : $ operator is invalid for atomic vectors
> 20081130 22:55:53| Retrieving SNP information annotations...done
> 20081130 22:55:53|Normalizing set for PCR fragment-length
> effects...done
>> cesFlnList[["GenomeWideSNP_6"]] <- cesFln;
> Error: object "cesFln" not found
>
> --------sessionInfo() and traceback()-------------------
>> sessionInfo()
> R version 2.7.0 (2008-04-22)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;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] DNAcopy_1.14.0 preprocessCore_1.2.0
> aroma.affymetrix_0.9.2
> [4] aroma.apd_0.1.3 R.huge_0.1.6 affxparser_1.12.2
> [7] aroma.core_0.9.2 sfit_0.1.5 aroma.light_1.9.2
> [10] digest_0.3.1 matrixStats_0.1.3 R.rsp_0.3.4
> [13] R.cache_0.1.7 R.utils_1.0.9 R.oo_1.4.3
> [16] R.methodsS3_1.0.1
>> traceback()
> 18: getChipType.AromaUnitTabularBinaryFile(ufl, ...)
> 17: getChipType(ufl, ...)
> 16: getChipType.UflSnpInformation(this)
> 15: getChipType(this)
> 14: sprintf("Chip type: %s", getChipType(this))
> 13: as.character.SnpInformation(x)
> 12: as.character(x)
> 11: print(as.character(x))
> 10: print.Object(...)
> 9: print(...)
> 8: eval.with.vis(expr, pf, NULL)
> 7: evalVis(expr)
> 6: capture.Verbose(this, print(...), level = level)
> 5: capture(this, print(...), level = level)
> 4: print.Verbose(verbose, si)
> 3: print(verbose, si)
> 2: process.FragmentLengthNormalization(fln, verbose = verbose)
> 1: process(fln, verbose = verbose)
>
>
> >
>
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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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