Hi Pierre, I think I know what units for now. I used units <- c(1:235834) and it worked.
Thanks, Ying On Thu, May 17, 2012 at 3:21 PM, sean nj <[email protected]> wrote: > Hi Pierre, > > Sorry to bother you again. > > I am following the Vignette: Creating binary data files containing copy > number estimates (http://www.aroma-project.org/node/88) and trying to > create a UGP file. But I am confused with the codes listed: > > units <- c(1,4,7); > ugp[units,1] <- 1; > > ugp[units,2] <- c(554268, 736483, 757922); > I tried to find some information regarding ugp, but had no success. My > question is what the units <- c(1,4,7)for? What does 1, 4, and 7 mean? > > I want to make a ugp file for Agilent UG-CGH-244A chip files I got from > TCGA-GBM data, which has 235834 probes. When I used units <- c(1,4,7), > > > mydata <- read.delim(file.choose()) > > mydata <- as.data.frame(mydata) > > str(mydata) > 'data.frame': 235834 obs. of 12 variables: > $ unitName > : Factor w/ 235834 levels "A_14_P100000",..: 12409 103695 103696 41581 > 41582 41583 41584 41585 41586 41587 ... > $ unitCount > : int 1 2 3 4 5 6 7 8 9 10 ... > $ Gene_Symbol > : Factor w/ 16808 levels "","1-Dec","1-Mar",..: 1 1 1 1 1 1 1 1 1 1 ... > $ Description > : Factor w/ 16670 levels "","1-acylglycerol-3-phosphate O-acyltransferase 1 > (lysophosphatidic acid acyltransferase, alpha)",..: 1 1 1 1 1 1 1 1 1 1 ... > $ Chromosome > : int 1 1 1 1 1 1 1 1 1 1 ... > $ chr_start > : int 604268 604287 689581 786483 792533 796956 807922 819590 834458 > 842413 ... > $ chr_end > : int 604327 604346 689640 786542 792586 797005 807966 819649 834517 > 842458 ... > $ Cytoband > : Factor w/ 259 levels "","hs|p11","hs|p11.1",..: 97 97 97 97 97 97 97 97 > 97 97 ... > $ > Reporter..genbank..Comment.OMOSOMAL_LOCATION..Comment.ACCESSION_STRING.: > Factor w/ 235649 levels ":::","::NC_000001.8[000786483..000786542]:",..: > 85381 85382 91604 2 3 4 101218 101217 87259 5 ... > $ Chr > : int 1 1 1 1 1 1 1 1 1 1 ... > $ Start_GRCH37 > : int 564405 564424 649718 746620 752670 757093 768059 779727 794595 > 802550 ... > $ End_GRCH37 > : int 564464 564483 649777 746679 752723 757142 768103 779786 794654 > 802595 ... > > units <- c(1,4,7) > > ugp[units,1] <- mydata$Chromosome > > ugp[units,2] <- mydata$chr_start > > print(ugp[units,]) > chromosome position > 1 1 604268 > 2 1 604287 > 3 1 689581 > Here I only got 3 probes, instead of 235834. > > > print(ugp[1:4,]) > chromosome position > 1 1 604268 > 2 NA NA > 3 NA NA > 4 1 604287 > > > > Here I am not sure where the NAs are from. > > Any suggestion? > > Thanks a lot for the help! > > Ying > > On Wednesday, May 16, 2012 4:19:31 PM UTC-4, sean nj wrote: > >> 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 <[email protected] >> > wrote: >> >>> Hi, >>> >>> On Wed, May 16, 2012 at 9:05 PM, sean nj <[email protected]> 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 <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 <[email protected]> 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 <[email protected]> >>> >> To unsubscribe and other options, go to http://www.aroma-project.org/ >>> **forum/ <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 <[email protected]> >>> > To unsubscribe and other options, go to http://www.aroma-project.org/* >>> *forum/ <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<[email protected]> >>> To unsubscribe and other options, go to http://www.aroma-project.org/** >>> forum/ <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 [email protected] > 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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