Re: [aroma.affymetrix] Error need help(CdfFile$byChipType)
HI Pierre, I did saved in the similar way (aroma.affymetrix/annotationData/Chip type/HuGene-1_0-st-v1/HuGene-1_0-st-v1,r3.CDF) but still i am coming up with same error. Thanks Vish On Tue, Aug 3, 2010 at 5:32 PM, Pierre Neuvial pie...@stat.berkeley.eduwrote: Hi, Most probably you haven't put the required CDF file in the corresponding annotationData/chipTypes/ directory. Have you read the vignette http://aroma-project.org/node/38 ? This is well explained there. Also, similar versions of this question have been answered on this list, see for example http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/d992f2ca51e71774/8ba42bb7bdbf1b48 Best Pierre. Be sure to put the CDF file in your annotationData/chipTypes/XX/ where XX is the platform you are using (e.g. HuGene-1_0-st-v1 for Human Gene 1.0 ST, HT_HG-U133_Plus_PM for the human PM plate arrays, etc.) On Tue, Aug 3, 2010 at 2:27 PM, vish ashwin4bioinformat...@gmail.com wrote: I am really new to this aroma.affymetrix. I am trying to analyze HuGene-1_0-st-v1 array and interested in Quality control check/ Assessment. when I am trying to run this command I am ending up with this error . Any help is greatly appreciated. cdf - AffymetrixCdfFile$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/
Re: [aroma.affymetrix] Error need help(CdfFile$byChipType)
HI Henrik, I could able to resolve my problem wrt CDF files but now i am struck with following error. cs - AffymetrixCelSet$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.eduwrote: 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$byChipType(chipType, tags = r3) Ashwin -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/ -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post
[aroma.affymetrix] Error need help(CdfFile$byChipType)
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$byChipType(chipType, tags = r3) Ashwin -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. You received this message because you are subscribed to the Google Groups aroma.affymetrix group with website http://www.aroma-project.org/. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe and other options, go to http://www.aroma-project.org/forum/
Re: [aroma.affymetrix] Error need help(CdfFile$byChipType)
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/
