Hi. On Fri, Oct 4, 2013 at 8:19 PM, Ann Loraine <alora...@gmail.com> wrote: > I am working with ATH1/GPL198 Affymetrix microarrays and would like to use > aroma to process a large set of arrays. > > I'm following the vignette on this page: > > http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis > > But am stuck at this step: > > chipType <- "HuGene-1_0-st-v1" > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3")
You need to place the http://aroma-project.org/setup > > What should I use for "chipType"? > > I tried "ATH1" and "GPL198" but got this error: > >> AffymetrixCdfFile$byChipType('ATH1',tags="r3") > [2013-10-04 23:17:44] Exception: Failed to create AffymetrixCdfFile object. > Could not locate an annotation data file for chip type 'ATH1' with tags 'r3' > and with filename extension 'cdf'. > > at #03. byChipType.UnitAnnotationDataFile(static, ...) > - byChipType.UnitAnnotationDataFile() is in environment > 'aroma.core' > > at #02. byChipType(static, ...) > - byChipType() is in environment 'aroma.core' > - originating from '<text>' > > at #01. AffymetrixCdfFile$byChipType("ATH1", tags = "r3") > - AffymetrixCdfFile$byChipType() is local of the calling function > > Error: Failed to create AffymetrixCdfFile object. Could not locate an > annotation data file for chip type 'ATH1' with tags 'r3' and with filename > extension 'cdf'. First, make sure to read http://aroma-project.org/setup/ so you understand where CDF file goes. The download the binary CDF that I've created: http://aroma-project.org/chipTypes/ATH1-121501 because the one that Affymetrix provides is in an ASCII format which is very slow to work with. The retry with: cdf <- AffymetrixCdfFile$byChipType("ATH1") You should not use an 'r3' tags, because the CDF has no such tag part of its filename. To understand what the term "tag" means, see http://aroma-project.org/definitions/. I strongly recommend that you make sure that you understand how filenames, directory names and fullname, name, tags are related - it really helps. /Henrik > > > -- > -- > 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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/groups/opt_out. -- -- 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/ --- You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group. To unsubscribe from this group and stop receiving emails from it, send an email to aroma-affymetrix+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/groups/opt_out.
