Hi Jim, Thanks a lot for all the detailed information. I did it with gcrma and all values were almost the same, but repeated with rma and worked well. Thanks a lot for all your efforts. Best, Nu On Wednesday, February 5, 2014 7:36 PM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Nu, Well, if I google gpl17417, I end up at this page: http://165.112.7.19/geo/query/acc.cgi?acc=GPL17417 which indicates that this is just an AraGene 1.1 ST array that they used a MNBI re-mapped cdf, from their version 16 set of packages. So now if I go there: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp I see this: *Version 16 (Data Sources <http: brainarray.mbni.med.umich.edu="" brainarray="" database="" customcdf="" 16="" .0.0="" version.html="">)* Sep 27, 2012, version 16 is released Custom CDF     R 2.15, BioC 2.11 So you could hypothetically use an old version of R and BioC. However, I prefer to stay in the here and now, so let's see what we can do: > library(BiocInstaller) Bioconductor version 2.12 (BiocInstaller 1.10.4), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help > biocLite(c("aragene11stattairgcdf","aragene11stattairgprobe")) BioC_mirror: http://bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.1. Installing package(s) 'aragene11stattairgcdf' 'aragene11stattairgprobe' Warning message: packages ‘aragene11stattairgcdf’, ‘aragene11stattairgprobe’ are not available (for R version 3.0.1) Hmmm. That's pretty bootleg. The MNBI site claims that version 17 works with BioC 2.12: *Version 17 (Data Sources <http: brainarray.mbni.med.umich.edu="" brainarray="" database="" customcdf="" 17="" .0.0="" version.html="">)* Apr 25, 2013, version 17 is released Custom CDF     R 2.15, BioC 2.11     R 3.0, BioC 2.12 In that case let's switch to R-3.0.2 and install by hand: > download.file("http://brainarray.mbni.med.umich.edu/Brainarray/Databas e/CustomCDF/17.1.0/tairg.download/aragene11stattairgcdf_17.1.0.tar.gz" , "./aragene11stattairgcdf_17.1.0.tar.gz") trying URL 'http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17 .1.0/tairg.download/aragene11stattairgcdf_17.1.0.tar.gz' Content type 'application/x-gzip' length 2258039 bytes (2.2 Mb) opened URL ================================================== downloaded 2.2 Mb > download.file("http://brainarray.mbni.med.umich.edu/Brainarray/Databas e/CustomCDF/17.1.0/tairg.download/aragene11stattairgprobe_17.1.0.tar.g z", "./aragene11stattairgprobe_17.1.0.tar.gz") trying URL 'http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/17 .1.0/tairg.download/aragene11stattairgprobe_17.1.0.tar.gz' Content type 'application/x-gzip' length 6983531 bytes (6.7 Mb) opened URL ================================================== downloaded 6.7 Mb > install.packages(c("aragene11stattairgprobe_17.1.0.tar.gz","aragene11s tattairgcdf_17.1.0.tar.gz"), repos=NULL) * installing *source* package ‘aragene11stattairgprobe’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (aragene11stattairgprobe) * installing *source* package ‘aragene11stattairgcdf’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (aragene11stattairgcdf) Now I don't see any celfiles on GEO to test, and to use gcrma will take some effort, as I already stated, but I can now at least run RMA on these data using the affy package with the re-mapped cdf. And if I just want to use oligo, I can > biocLite("pd.aragene.1.1.st") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.2. Installing package(s) 'pd.aragene.1.1.st' trying URL 'http://bioconductor.org/packages/2.13/data/annotation/src/contrib/pd. aragene.1.1.st_3.8.0.tar.gz' Content type 'application/x-gzip' length 34310175 bytes (32.7 Mb) opened URL ================================================== downloaded 32.7 Mb * installing *source* package ‘pd.aragene.1.1.st’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE pd.aragene.1.1.st) The downloaded source packages are in ‘/tmp/RtmpMlVUZN/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done > Best, Jim On 2/5/2014 11:24 AM, n omranian wrote: > > Hi Jim, > > Thanks for the reply. > > yes, this is a warning but when I use exp_data <- gcrma(affydata), it > gives me this error. > > Also if I use oligo, I couldn't find a way to map my probe ids. I mean > I have the CDF file, but it is useless. So, the most important thing > for me is the mapping and applying normalization on my affy data. > > > Adjusting for optical effect..............................Done. > Computing affinities[1] "Checking to see if your internet connection > works..." > [1] "Environment gpl17417aragene10stattairgcdfcdf was not found in the > Bioconductor repository." > [1] "Checking to see if your internet connection works..." > [1] "Environment gpl17417aragene10stattairgcdfprobe was not found in > the Bioconductor repository." > Error in get(probepackagename) : > object 'gpl17417aragene10stattairgcdfprobe' not found > > > Thanks, > Nu > > > > On Wednesday, February 5, 2014 5:18 PM, James W. MacDonald > <jmacdon@uw.edu> wrote: > Hi Nu, > > On 2/5/2014 9:42 AM, n omranian wrote: > > Hi All, > > > > I have a problem reading my cel files. > > My data is from Arabidopsis thaliana and the platform is GPL17417. > > > > I get the cdf file for this platform, which is > GPL17417_aragene10st_At_TAIRG and installed it in R. > > > > But still when I read the cel files I get the error as follows: > >> affydata <- ReadAffy(cdfname="gpl17417aragene10stattairgcdf") > > > > Warning message: > > > > > > > > The affy package can process data from the Gene ST 1.x series of arrays, > > but you should consider using either the oligo or xps packages, > which are specifically > > designed for these arrays. > > That's not an error. It's a warning. Is there something about this > warning that is unclear? The goal is to explain that you should really > be using oligo or xps for these arrays. > > > > > > > and when I use read.affy (simpleaffy) it gives me this error: > > read.affy() Error in file(file, "rt") : cannot open the connection > In addition: Warning message: In file(file, "rt") : cannot open file > './covdesc': No such file or directory > > > > I want to read my cel files and normalize them with gcrma. > > The simpleaffy error is insurmountable, as simpleaffy is designed > specifically for 3'-biased arrays. If you want to do quality control, > perhaps you should try the arrayQualityMetrics package. > > In addition, using gcrma with PM-only arrays is not a trivial task. > Unless you are willing to do the research to figure out how to do it, I > would recommend you follow the warning above and use oligo or xps to > analyze these data. > > Best, > > Jim > > > > > > > I would appreciate if anybody could help me. > > Thanks, > > Nu > > > > > [[alternative HTML version deleted]] > > > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]]

Hi Guido, You helped me a lot. Thanks a lot indeed.... What would you suggest for the normalization, would it be enough to to rma? or any vsn preprocessing? Thanks a lot again. Nu On Wednesday, February 5, 2014 6:11 PM, "Hooiveld, Guido" <guido.hooiveld@wur.nl> wrote: Hi Nu, I noticed that the GEO accession number reflects an alternative (custom) CDF (chip definition file; mapping) of the AraGene10st array. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL17417 The CDF file available at GEO cannot (directly) be used with BioC. You better download the custom CDF and corresponding probe file directly from the MBNI group (http://brainarray.mbni.med.umich.edu/Brainarray/D atabase/CustomCDF/CDF_download.asp#v16), as is also indicated at the GEO web page. Note that the current version is 18. Manhong (creator of the custom CDFs) and Benilton (author oligo package) said they are working on the implementation of the custom CDFs in the oligo framework. Until this is done, you can (should) use the affy library to read the data, and specify this CDF "aragene10stattairg" when calling ReadAffy() [affy.data <- ReadAffy(cdfname = "aragene10stattairg")]. Also, like Jim said, gcrma analysis with a PM-only array is rather complex and usually not done... HTH, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email:      guido.hooiveld@wur.nl internet:  http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of n omranian Sent: Wednesday, February 05, 2014 17:24 To: James W. MacDonald Cc: bioconductor@r-project.org Subject: Re: [BioC] error ReadAffy Hi Jim, Thanks for the reply. yes, this is a warning but when I use exp_data <- gcrma(affydata), it gives me this error. Also if I use oligo, I couldn't find a way to map my probe ids. I mean I have the CDF file, but it is useless. So, the most important thing for me is the mapping and applying normalization on my affy data. Adjusting for optical effect..............................Done. Computing affinities[1] "Checking to see if your internet connection works..." [1] "Environment gpl17417aragene10stattairgcdfcdf was not found in the Bioconductor repository." [1] "Checking to see if your internet connection works..." [1] "Environment gpl17417aragene10stattairgcdfprobe was not found in the Bioconductor repository." Error in get(probepackagename) :   object 'gpl17417aragene10stattairgcdfprobe' not found Thanks, Nu On Wednesday, February 5, 2014 5:18 PM, James W. MacDonald <jmacdon@uw.edu> wrote: Hi Nu, On 2/5/2014 9:42 AM, n omranian wrote: > Hi All, > > I have a problem reading my cel files. > My data is from Arabidopsis thaliana and the platform is GPL17417. > > I get the cdf file for this platform, which is GPL17417_aragene10st_At_TAIRG and installed it in R. > > But still when I read the cel files I get the error as follows: >> affydata <- ReadAffy(cdfname="gpl17417aragene10stattairgcdf") > > Warning message: > > > > The affy package can process data from the Gene ST 1.x series of > arrays, but you should consider using either the oligo or xps > packages, which are specifically designed for these arrays. That's not an error. It's a warning. Is there something about this warning that is unclear? The goal is to explain that you should really be using oligo or xps for these arrays. > > > and when I use read.affy (simpleaffy) it gives me this error: > read.affy() Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") :   cannot open file './covdesc': No such file or directory > > I want to read my cel files and normalize them with gcrma. The simpleaffy error is insurmountable, as simpleaffy is designed specifically for 3'-biased arrays. If you want to do quality control, perhaps you should try the arrayQualityMetrics package. In addition, using gcrma with PM-only arrays is not a trivial task. Unless you are willing to do the research to figure out how to do it, I would recommend you follow the warning above and use oligo or xps to analyze these data. Best, Jim > > I would appreciate if anybody could help me. > Thanks, > Nu > >     [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099     [[alternative HTML version deleted]] [[alternative HTML version deleted]]