Hi. On Tue, Jun 12, 2012 at 1:17 AM, dave <[email protected]> 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 [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. 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/
