Hi. On Wed, May 26, 2010 at 3:24 PM, Ivanek, Robert <robert.iva...@fmi.ch> wrote: > Dear Sir or Madam, > > I would like to analyse the copy number variation data from Affymetrix > Mouse Diversity Array. I have not found any information on your website > about this particular array.
I have created page for this: http://aroma-project.org/chipTypes/MOUSEDIVm520650 > I have tried to build the annotation files > which are required by aroma but without success. I have few questions > regarding that: > > 1: Is aroma.affymetrix able to analyse the "Mouse Diversity Array" ? Yes, because there should be no reason why it shouldn't - it uses a standard CDF etc. As you've noted, UGP (and UFL) files have not been created by anyone yet. For CN analysis, at least the UGP (genome positions) annotation data file needs to be there. > > 2: I tried to build the "UGP" file directly from NetAffx annotation > files using the code on your website, however I am getting the following > error. > > ## > library("aroma.affymetrix") > ## > ## create UGP from NetAffx files > cdf <- AffymetrixCdfFile$byChipType("MOUSEDIVm520650") > ## > ## Creates an empty UGP file for the CDF, if missing. > ugp <- AromaUgpFile$allocateFromCdf(cdf, tags=c("na30", "RI20100526")) > ## > ## Import NetAffx unit position data > csv <- AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", > otags=".na30") > > Error in list(`AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", > tags = ".na30")` = <environment>, : > > [2010-05-26 15:11:00] Exception: File format error of the tabular file > ('annotationData/chipTypes/MOUSEDIVm520650/NetAffx/MOUSEDIVm520650.na30.annot.csv'): > \ > line 1 did not have 12 elements > at throw(Exception(...)) > at throw.default("File format error of the tabular file ('", > getPathname(this), "'): ", ex$message) > at throw("File format error of the tabular file ('", > getPathname(this), "'): ", ex$message) > at value[[3]](cond) > at tryCatchOne(expr, names, parentenv, handlers[[1]]) > at tryCatchList(expr, classes, parentenv, handlers) > at tryCatch({ > at verify.TabularTextFile(this, ...) > at verify(this, ...) > at this(...) > at newInstance.Class(clazz, ...) > at newInstance(clazz, ...) > at newInstance.Object(static, pathname) > at newInstance(static, pathname) > at method(static, ...) > at AffymetrixNetAffxCsvFile$byChipType("MOUSEDIVm520650", tags = > ".na30") > In addition: Warning message: > In read.table(3L, header = TRUE, colClasses = c(NA_character_, > NA_character_, : > not all columns named in 'colClasses' exist I had a look at the MOUSEDIVm520650.na30.annot.csv file. The line containing column names, that is: "Probe Set ID","dbSNP RS ID","Chromosome","Physical Position","Strand","Cytoband","Allele A","Allele B","Associated Gene","Genetic Map","Fragment Enzyme Type Length Start Stop", contains a trailing comma (,) that shouldn't be there ("file format error"). This cause R to think there should be 12 and not 11 columns in the data set. Open the file in an editor and remove that trailing comma and any whitespace after "Fragment Enzyme Type Length Start Stop". Then save the file. That should solve the problem. The other CSV file - MOUSEDIVm520650.cn.na30.annot.csv - does not have this problem. > > > 3. I tried it also by using the "manual" approach using the > tab=delimited file, however it seems to me that the mitochondria probes > are skipped (NA values in ugp[,1] but valid values in ugp[,2]). The Affymetrix NetAffx CSV files use s "M" for the mitochondria chromosome. In aroma we encode this by integer 25. > Another > problem is that some positions for other chromosomes are not loaded in > properly (valid values in ugp[,1] but NA values in ugp[,2]). You don't show how you read the data "manually", so it is hard to say what you are doing wrong here. But note that there are quite a few arguments in read.table() that you need to set correctly in order to read Affymetrix NetAffx CSV files (it doesn't make easier that Affymetrix changes the file format once in a while and have stray erroneous symbols such as the above comma). Also, search our forum for 'MOUSEDIVm520650', because about a year ago David Rosenberg disscussed this chip type and I think he did create various annotation data files for the chip type. This was before the chip type was publicly announced by Affymetrix. /Henrik > > > Here is the sessionInfo: > > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C > [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C > LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] aroma.affymetrix_1.6.0 aroma.apd_0.1.7 affxparser_1.20.0 > R.huge_0.2.0 aroma.core_1.6.0 aroma.light_1.16.0 > [7] matrixStats_0.2.1 R.rsp_0.3.6 R.cache_0.3.0 > R.filesets_0.8.1 digest_0.4.2 R.utils_1.4.0 > [13] R.oo_1.7.2 R.methodsS3_1.2.0 RColorBrewer_1.0-2 > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > > > > Best Regards > > Robert > > > > > > -- > Robert Ivanek > Postdoctoral Fellow Schuebeler Group > Friedrich Miescher Institute > Maulbeerstrasse 66 > 4058 Basel / Switzerland > Office phone: +41 61 697 6100 > > -- > 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/
