Question

error in AffyTiling package

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zhen tao ▴ 30

@zhen-tao-3317

Last seen 10.2 years ago

Hi: I'm trying to use AffyTiling package to normalize my tiling array data. However, it shows the error below (hightlighted in yellow) when I run the function AnalyzeTilingCelFiles. Does anybody know how to deal with this? Thanks!!!! > NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"), "At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv") [1] "Importing BPMAP file." [1] "Reading CEL Files & Extracting Intensities." [1] "Quantile normalizing/ log(2) transform." [1] "Finalizing data." Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Tao Zhen Plant Functional Genomics Group DBS NUS [[alternative HTML version deleted]]

AffyTiling AffyTiling • 1.1k views

ADD COMMENT • link updated 14.9 years ago by Charles Danko ▴ 40 • written 14.9 years ago by zhen tao ▴ 30

score 0 · Answer 1 · 2009-12-28

Hi, Zhen, It looks a known issue that is fixed in later versions of the package. You will need to be using a version >= 1.4.1; you can check by typing "sessionInfo()" into your R terminal. You will also have to tell AffyTiling not to limit the analysis to NCBI coordinates. You can do this by editing your command as follows: > NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"), * readOnlyNCBI=FALSE,* "At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv") Please write back if you continue to have problems! Good luck! Best, Charles Message: 4 Date: Mon, 28 Dec 2009 15:11:23 +0800 From: zhen tao <jennytz8@gmail.com> Subject: [BioC] error in AffyTiling package To: bioconductor@stat.math.ethz.ch Message-ID: <8b7b0b050912272311s3f10fecm2ccab94cfe594261@mail.gmail.com> Content-Type: text/plain Hi: I'm trying to use AffyTiling package to normalize my tiling array data. However, it shows the error below (hightlighted in yellow) when I run the function AnalyzeTilingCelFiles. Does anybody know how to deal with this? Thanks!!!! > NORM <- AnalyzeTilingCelFiles(dir(pattern=".cel|.CEL"), "At35b_MR_v04-2_TIGRv5.bpmap", outfilename="normalizedata.tsv") [1] "Importing BPMAP file." [1] "Reading CEL Files & Extracting Intensities." [1] "Quantile normalizing/ log(2) transform." [1] "Finalizing data." Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent Tao Zhen Plant Functional Genomics Group DBS NUS -- Postdoctoral Fellow Cornell University 102D Weill Hall Ithaca, NY 14853 Phone (Lab, 467 Biotech Bldg.): 607-255-4743 E-mail: dankoc@gmail.com [[alternative HTML version deleted]]