Thanks for that Henrik i could able to solve that On Thu, Aug 5, 2010 at 2:53 PM, Henrik Bengtsson <h...@stat.berkeley.edu>wrote:
> See if the new troubleshooting page 'Setup of directory structures': > > http://aroma-project.org/troubleshooting/DirectoryStructures > > will help you. > > /Henrik > > On Thu, Aug 5, 2010 at 8:47 PM, ashwin Vishnuvardhana > <ashwin4bioinformat...@gmail.com> wrote: > > HI Henrik, > > I could able to resolve my problem wrt CDF files but now i am struck with > > following error. > >> cs <- AffymetrixCelSet$byName("tissues", cdf=cdf) > > Error in list(`AffymetrixCelSet$byName("tissues", cdf = cdf)` = > > <environment>, : > > > > [2010-08-05 13:38:14] Exception: Cannot create AffymetrixCelSet. No such > > directory: tissues/HuGene-1_0-st-v1 > > at throw(Exception(...)) > > at throw.default("Cannot create ", class(static)[1], ". No such > > directory: ", path) > > at throw("Cannot create ", class(static)[1], ". No such directory: ", > > path) > > at method(static, ...) > > at AffymetrixCelSet$byName("tissues", cdf = cdf) > >> > > I would like to know what directory i should create for getting rid of > this > > error > > > > Thanks > > Vish > > > > > > > > On Thu, Aug 5, 2010 at 1:10 PM, ashwin Vishnuvardhana > > <ashwin4bioinformat...@gmail.com> wrote: > >> > >> 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/ > > > > -- > 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. 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