Hi, you write:
annotationData/Chip type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF but that is *not* was is documented or written in the vignettes. You should have: annotationData/chipTypes/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF It is really important that you use the correct directory names exactly like that. /Henrik On Thu, Aug 5, 2010 at 7:34 PM, ashwin Vishnuvardhana <ashwin4bioinformat...@gmail.com> wrote: > HI Pierre, > I did saved in the similar way (aroma.affymetrix/annotationData/Chip > type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF) > but still i am coming up with same error. > > Thanks > Vish > > On Tue, Aug 3, 2010 at 5:32 PM, Pierre Neuvial <pie...@stat.berkeley.edu> > wrote: >> >> Hi, >> >> Most probably you haven't put the required CDF file in the >> corresponding annotationData/chipTypes/ directory. >> >> Have you read the vignette http://aroma-project.org/node/38 ? This is >> well explained there. >> >> Also, similar versions of this question have been answered on this >> list, see for example >> >> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d992f2ca51e71774/8ba42bb7bdbf1b48 >> >> Best >> >> Pierre. >> >> >> Be sure to put the CDF file in your annotationData/chipTypes/XX/ where >> XX is the platform you are using (e.g. HuGene-1_0-st-v1 for Human >> Gene 1.0 ST, HT_HG-U133_Plus_PM for the human PM plate arrays, etc.) >> >> On Tue, Aug 3, 2010 at 2:27 PM, vish <ashwin4bioinformat...@gmail.com> >> wrote: >> > >> > I am really new to this aroma.affymetrix. I am trying to analyze >> > HuGene-1_0-st-v1 array and interested in Quality control check/ >> > Assessment. >> > when I am trying to run this command I am ending up with this error . >> > Any help is greatly appreciated. >> > >> > cdf <- AffymetrixCdfFile$byChipType(chipType, tags="r3") >> > Error in list(`AffymetrixCdfFile$byChipType(chipType, tags = "r3")` = >> > <environment>, : >> > >> > [2010-08-03 16:23:44] Exception: Could not locate a file for this chip >> > type: HuGene-1_0-st-v1,r3 >> > at throw(Exception(...)) >> > at throw.default("Could not locate a file for this chip type: ", >> > paste(c(chipType, tags), collapse = ",")) >> > at throw("Could not locate a file for this chip type: ", >> > paste(c(chipType, tags), collapse = ",")) >> > at method(static, ...) >> > at AffymetrixCdfFile$byChipType(chipType, tags = "r3") >> > >> > Ashwin >> > >> > -- >> > 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/ > > -- > 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/
