HI but still I have a problem, These are steps i am doing 1. My current directory is on desktop where exactly my raw data is 2. then I am trying to use the command in aroma.project 3. I did changed the directory as you mentioned
And the error remains same. I have one question do we convert cdf (text) file to binary ? I downloaded it from aroma project website. Thanks Vish On Thu, Aug 5, 2010 at 12:38 PM, Henrik Bengtsson <h...@stat.berkeley.edu>wrote: > 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/ > -- 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/
