Hi, before anything else, what are the problems you're experiencing with the official Affymetrix CDF file:
> I know I can download a cdf file from the Affymetrix website, but that > file doesn't work for me.. That CDF has been used for many year and yet I haven't heard anyone else having problems with it. There is probably a simple reason and solution for your problems. Let us know what's not working and we'll help you. About writeCdf(): writeCdf() is a cleanup version of community contributed pdInfo2Cdf() with the difference that writeCdf() is easier to use. I missed to flag it an early-beta version, because it hasn't undergone rigorous testing on multiple chip types; it [pdInfo2Cdf()] was original designed for expression arrays and has hence only been used/tested for such. My best guess is that the current code does not work SNP chips. I add it to the todo list. Hope this helps /Henrik On Fri, Jan 28, 2011 at 1:25 AM, Sake van Pelt <tlep.nav.eka...@gmail.com> wrote: > Hi all, > > I'm trying to extract a cdf file from the R platform design package of > the Affymetrix 250k_Nsp array. I used the writeCdf.AffyGenePDInfo > function. > This is my code: > >>library(aroma.affymetrix) >>library(pd.mapping250k.nsp) >>library(affxparser) >>library(pdInfoBuilder) >>writeCdf.AffyGenePDInfo(pd.mapping250k.nsp) > > It starts very promising: > > Generating CDF file from Platform Design (PD) package... > Platform Design (PD) package: pd.mapping250k.nsp > Output path: annotationData/chipTypes/Mapping250K_Nsp > Filename: Mapping250K_Nsp.cdf > Pathname to generated CDF: annotationData/chipTypes/Mapping250K_Nsp/ > Mapping250K_Nsp.cdf > Chip type: Mapping250K_Nsp > Tags: > Chip type dimensions: 2560x2560 > Total number of cells (probes): 6553600 > Querying Platform Design database... > 'data.frame': 3221600 obs. of 7 variables: > $ fid : int 2566 2568 2570 2572 2574 2576 2578 2580 2582 > 2584 ... > $ strand: int 0 1 1 0 1 0 0 0 0 0 ... > $ allele: int 0 0 1 0 1 0 0 0 0 1 ... > $ fsetid: int 258185 192040 236691 139532 24150 41056 185256 > 133631 258800 234975 ... > $ pos : int 4 7 7 2 9 5 3 1 4 5 ... > $ x : int 5 7 9 11 13 15 17 19 21 23 ... > $ y : int 1 1 1 1 1 1 1 1 1 1 ... > Number of cells (probes) in PD database: 3221600 (49.16%) of 6553600 > Querying Platform Design database...done > Creating list from query table... > Number of units: 262264 > Average number of cells per units: 12.28 > Creating list from query table...done > Setting up CDF tree structure... > Setting CDF header... > Setting CDF header...done > Setting up CDF units... > Number of units: 262264 > > But then I get the following message: > > Error in order(u$atom) : argument 1 is not a vector > >> sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] 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] pdInfoBuilder_1.14.1 pd.mapping250k.nsp_1.1.0 > oligoClasses_1.12.2 > [4] Biobase_2.10.0 RSQLite_0.9-4 DBI_0.2-5 > [7] aroma.affymetrix_1.9.0 aroma.apd_0.1.7 > affxparser_1.22.1 > [10] R.huge_0.2.0 aroma.core_1.9.1 > aroma.light_1.18.2 > [13] matrixStats_0.2.2 R.rsp_0.4.1 R.cache_0.3.0 > [16] R.filesets_0.9.1 digest_0.4.2 R.utils_1.6.0 > [19] R.oo_1.7.4 oligo_1.14.0 > R.methodsS3_1.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 Biostrings_2.18.2 IRanges_1.8.8 > [4] preprocessCore_1.12.0 splines_2.12.0 > >> traceback() > No traceback available > > I know I can download a cdf file from the Affymetrix website, but that > file doesn't work for me.. > I hope someone can help me! > > Kind regards, > > Sake van Pelt > Graduating Bio-Informatics student at the University of Applied > Sciences in Leiden, Netherlands > > -- > 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/
