Actually, there is a much easier way to create the CDF; one can create one from the corresponding PD package from Bioconductor. I did that and made it available at:
http://aroma-project.org/chipTypes/HuGene-1_1-st-v1 A small disclaimer: I haven't verified it on real data, but similar conversions have done before so everything "should be ok". /Henrik On Wed, Jun 13, 2012 at 5:24 PM, Henrik Bengtsson <henrik.bengts...@aroma-project.org> wrote: > Hi. > > On Tue, Jun 12, 2012 at 1:17 AM, dave <davidarteta2...@gmail.com> wrote: >> Hi, >> >> I hope I am not asking a too simple question but I am trying to load >> affy HuGene-1_1-st-v1 chips on aroma.affymetrix. I have been away from >> affy analysis for a while so maybe this is a known thing. I cannot >> find the corresponding cdf file (in affymetrix webpage they seem to >> have modified the files). I tried with the HuGene-1_0-st-v1 cdf file >> (which seems to work for dChip analysis) renaming it but gave me an >> error: >> >>> cdf <- AffymetrixCdfFile$byChipType("HuGene-1_1-st-v1") >>> cdf >> AffymetrixCdfFile: >> Path: annotationData/chipTypes/HuGene-1_1-st-v1 >> Filename: HuGene-1_1-st-v1.cdf >> Filesize: 16.67MB >> Chip type: HuGene-1_1-st-v1 >> RAM: 0.00MB >> File format: v4 (binary; XDA) >> Dimension: 1050x1050 >> Number of cells: 1102500 >> Number of units: 33252 >> Cells per unit: 33.16 >> Number of QC units: 0 >>> chipType <- "HuGene-1_1-st-v1" >>> cs <- AffymetrixCelSet$byName("Samples", cdf=cdf) >> Error en method(static, ...) : >> [2012-06-11 17:15:28] Exception: Failed to setup a data set for any of >> 1 data directories located. The following reasons were reported: (1) >> Cannot set CDF. The specified CDF structure ('HuGene-1_1-st-v1') is >> not compatible with the chip type ('HuGene-1_1-st-v1') of the CEL >> file. The number of cells do not match: 1102500 != 1178100 (while >> trying 'rawData/Samples/HuGene-1_1-st-v1'). > > Yes, that won't work; HuGene-1_1-st-v1 and HuGene-1_0-st-v1 are > completely different chip types with incompatible CDFs. > > It appears that Affymetrix does not provide a CDF for the > HuGene-1_1-st-v1 chip type. However, they do provide > HuGene-1_1-st-v1.r4.PGF and HuGene-1_1-st-v1.r4.CLF files (part of > their 'HuGene-1_1-st-v1_strip_libraryfile.zip' library file available > on their website). It should be possible to create a CDF from these > file. At the moment, there is not such support built into > aroma.affymetrix, but you could use the Perl scripts provided by > Elizabeth Purdom and Mark Robinson, see How To page 'Create a CDF file > from scratch (or from CLF and PGF files)' > [http://aroma-project.org/node/40]. > > Hope this helps > > /Henrik > >> >> Can anyone help me? >> >> Thanks >> >> Dave >> >> >>> sessionInfo() >> R version 2.14.1 (2011-12-22) >> Platform: i386-pc-mingw32/i386 (32-bit) >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] hugene11stv1hsentrezgcdf_15.1.0 AnnotationDbi_1.16.19 >> Biobase_2.14.0 >> [4] aroma.affymetrix_2.5.0 affxparser_1.26.4 >> aroma.apd_0.2.2 >> [7] R.huge_0.3.0 aroma.core_2.5.0 >> aroma.light_1.22.0 >> [10] BiocInstaller_1.2.1 matrixStats_0.5.0 >> R.rsp_0.7.5 >> [13] R.cache_0.6.2 R.filesets_1.1.5 >> digest_0.5.2 >> [16] R.utils_1.12.1 R.oo_1.9.3 >> affy_1.32.1 >> [19] R.methodsS3_1.2.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.22.0 DBI_0.2-5 IRanges_1.12.6 >> preprocessCore_1.16.0 RSQLite_0.11.1 >> [6] tools_2.14.1 zlibbioc_1.0.1 >> >> -- >> 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/
