Hi Pierre, I figured out what's wrong. I did not set the object unitNames.
After I ran > unitNames <- getUnitNames(unf) > units <- indexOf(unf,names=unitNames) it works now. Thanks, Ying On Wed, May 16, 2012 at 3:44 PM, Pierre Neuvial <pie...@stat.berkeley.edu>wrote: > Hi, > > On Wed, May 16, 2012 at 9:05 PM, sean nj <njs...@gmail.com> wrote: > > > > Hi, > > > > I did get rid of the error message when I ran : > > > > > unf <- > TextUnitNamesFile$byChipType(chipType) > > > > I got this done by loading the aroma.affymetrix package, in addition to > aroma.core. > > > > But now I got another error message when I followed Henrik's code at > http://aroma-project.org/node/88 > > > > I was trying to creating data files containing log2 CN ratios. > Everything was fine until I ran > > > > > units <- indexOf(unf, unitNames) > > Error in indexOf.UnitNamesFile(unf, unitNames) : > > [2012-05-16 14:53:18] Exception: If specified, argument 'pattern' must > be a single string. Did you mean to use argument 'names'? > > at #02. indexOf.UnitNamesFile(unf, unitNames) > > - indexOf.UnitNamesFile() is in environment 'aroma.core' > > at #01. indexOf(unf, unitNames) > > - indexOf() is in environment 'R.filesets' > > > > > > > From the error message (pretty explicit) it looks like you should have > done > > units <- indexOf(unf, names=unitNames) > > instead of > > units <- indexOf(unf, unitNames) > > That's what you do below. > > Cheers, > > Pierre > > > The command ran successfully when I tried to get units for certain probes > > > > > units <- indexOf(unf, names=c("A_16_P15025341","A_16_P00013121") > > + ) > > > units > > [1] 1006 1019 > > > > > I tried > ?indexOf.UnitNamesFile() and here is what I got: > > > > indexOf(this, pattern=NULL, names=NULL, ...) > > > > Arguments > > > > pattern A pattern to be used for identifying unit names of interest. > If NULL, no regular expression matching is done. > > > > > > > > names Names to be match exactly to the unit names. > > > > ... Not used. > > > > > > What did I do wrong? > > > > Thanks a lot for the help! > > > > Ying > > > > > sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > > [1] aroma.affymetrix_2.5.0 affxparser_1.28.0 > aroma.apd_0.2.2 R.huge_0.3.0 > > [5] aroma.core_2.5.0 aroma.light_1.24.0 > matrixStats_0.5.0 R.rsp_0.7.5 > > [9] R.filesets_1.1.5 digest_0.5.2 > R.cache_0.6.2 R.utils_1.12.1 > > [13] R.oo_1.9.3 R.methodsS3_1.2.2 > > loaded via a namespace (and not attached): > > [1] tools_2.15.0 > > > > > > > > > On Tue, May 15, 2012 at 12:38 PM, sean nj <njs...@gmail.com> wrote: > >> > >> Hi guys, > >> > >> I was following the Vignette: Creating binary data files containing > copy number estimates and trying to work on agilent HG-CGH-244A chip. I > downloaded and unzipped the .gz of the > HG-CGH-244A,TCGA,HB20080512,unitNames.txt and > HG-CGH-244A,TCGA,HB20080512.ugp and put them in > H:\Aroma_Analysis\annotationData\chipTypes\HG-CGH-244A folder. Then I tried > to run the same code on the vignette and got the error right away (please > see end of this email). Did I do something wrong? > >> > >> I have one more question regarding "Creating data files containing log2 > CN ratios" with HG-CGH-244A chip. The data I have are level 2 files from > TCGA. There is one txt file for each sample (not the original .asb > file) and its format is like: > >> > >> > >> Hybridization REF MSK_00001_251469322729_S01_CGH-v4_91 > >> > >> Composite Element REF normalizedLog2Ratio > >> > >> A_14_P112718 0.135431541355747 > >> > >> A_16_P15000916 0.441719513563848 > >> > >> A_16_P15001074 0.227252175271962 > >> > >> A_16_P00000012 0.231158251618718 > >> > >> A_16_P00000014 -0.0623833233443793 > >> > >> ......................................................... > >> > >> .......................................................... > >> > >> My first question is, does this kind data file work? > >> > >> My second question is, do I need to create a folder rawCnData as > mentioned in the vignette (Pathname: > rawCnData/MyDataSet,tagA,tagB/HG-CGH-244A/SampleA,tagA,tagB,log2ratio,total.asb)? > I also have the rawData folder which holds affy snp6 and expression data. > >> > >> > >> > >> Thanks a lot for the help! > >> > >> > >> > >> Ying > >> > >> > library(aroma.core) > >> > chipType <- "HG-CGH-244A" > >> > unf <- TextUnitNamesFile$byChipType(chipType) > >> Error in method(static, ...) : > >> [2012-05-15 12:12:26] Exception: Failed to create TextUnitNamesFile > object. Could to locate an annotation data file for chip type 'HG-CGH-244A' > (without requiring any tags) and with filename extension 'names' (this may > not be the correct extension as it was guessed from the class name > 'TextUnitNamesFile'). > >> > >> at #02. method(static, ...) > >> - method() is in environment 'aroma.core' > >> at #01. TextUnitNamesFile$byChipType(chipType) > >> - TextUnitNamesFile$byChipType() is local of the calling > function > >> > sessionInfo() > >> R version 2.15.0 (2012-03-30) > >> Platform: x86_64-pc-mingw32/x64 (64-bit) > >> locale: > >> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > >> [5] LC_TIME=English_United States.1252 > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> other attached packages: > >> [1] aroma.core_2.5.0 aroma.light_1.24.0 matrixStats_0.5.0 > R.rsp_0.7.5 R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2 > R.utils_1.12.1 > >> [9] R.oo_1.9.3 R.methodsS3_1.2.2 > >> > > >> > >> > >> > >> -- > >> 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. > >> > >> > >> You received this message because you are subscribed to the Google > Groups "aroma.affymetrix" group with website http://www.aroma-project.org/ > . > >> To post to this group, send email to aroma-affymetrix@googlegroups.com > >> To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > > > > > -- > > 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. > > > > > > You received this message because you are subscribed to the Google > Groups "aroma.affymetrix" group with website http://www.aroma-project.org/ > . > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > -- > 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. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > -- 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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