Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 * chipType - HG-U133_Plus_2* * chipTypeS - gsub(,.*, , chipType)* * path - Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE) * *Error in getReadablePath.Arguments(static, ...) : * * object 'pathAC' not found* On Wednesday, May 1, 2013 1:22:08 PM UTC+1, nawin MOHAMMED wrote: I also tried put the cdf file in the HG-U133_Plus_2 folder directly as u see in the path but same error * pathAC - Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist=TRUE)* *[2013-05-01 13:20:42] Exception: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2')* * * * at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, * ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 On Wednesday, May 1, 2013 1:13:18 PM UTC+1, nawin MOHAMMED wrote: Hi Henrik i changed the directory as you told me but i got this error ?? ' pathAC - Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 13:11:50] Exception: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/ChipType/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/ChipType/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' getwd() [1] C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2 I don't know why that happen On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote: Hi. On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED naw...@gmail.com wrote: hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma : Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type chipType in a directory of format: annotationData/chipTypes/chip type/ and my location is C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 i just creat new folder in annotation data with name chip type and inside it another folder with chip name ??? iam just confused ?? What you're missing in Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory is the part that says ***of the current working directory***. In other words, in your current working directory (i.e. getwd()) you should see subdirectory annotationData if you call list.files(). You may find the following page useful too:
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
Hi, Please respect the people who are trying to help you out by not sending an email to the list every time you are trying a new (random) command, especially since you are not following the advice which is given to you. As Henrik suggested, 1. put your data files (annotationData/, rawData/, etc.) in C:/Users/nwayyin/AromaAnalysis/ This means that you should have: C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2 This is not what you have right now ! and then, still quoting Henrik, 2. let that be your working directory in R. This means that getwd() should say C:/Users/nwayyin/AromaAnalysis This is not what you did either ! Please make sure that you did what has been suggested. Thanks, Pierre On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED nawi...@gmail.com wrote: getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 chipType - HG-U133_Plus_2 chipTypeS - gsub(,.*, , chipType) path - Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE) Error in getReadablePath.Arguments(static, ...) : object 'pathAC' not found On Wednesday, May 1, 2013 1:22:08 PM UTC+1, nawin MOHAMMED wrote: I also tried put the cdf file in the HG-U133_Plus_2 folder directly as u see in the path but same error pathAC - Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 13:20:42] Exception: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 On Wednesday, May 1, 2013 1:13:18 PM UTC+1, nawin MOHAMMED wrote: Hi Henrik i changed the directory as you told me but i got this error ?? ' pathAC - Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 13:11:50] Exception: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/ChipType/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/ChipType/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' getwd() [1] C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2 I don't know why that happen On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote: Hi. On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED naw...@gmail.com wrote: hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma : Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type chipType in a
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
Iam so sorry thank u and i am grateful , but iam just trying solve my error .?? and this is also not working again , ok \i create a folder in user\nwayyin\ the name is (AromaAnalysis) then i create another folder with name annotationData then another folder with HG-U133_Plus_2 which contain CDF file as bellow : getwd() [1] C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2 library(R.utils) pathAC - Arguments$getReadablePath(annotationData/chipTypes/, mustExist=TRUE) [2013-05-01 15:31:49] Exception: Pathname not found: annotationData/chipTypes (none of the parent directories [annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') On Wednesday, May 1, 2013 1:34:30 PM UTC+1, Pierre Neuvial wrote: Hi, Please respect the people who are trying to help you out by not sending an email to the list every time you are trying a new (random) command, especially since you are not following the advice which is given to you. As Henrik suggested, 1. put your data files (annotationData/, rawData/, etc.) in C:/Users/nwayyin/AromaAnalysis/ This means that you should have: C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2 This is not what you have right now ! and then, still quoting Henrik, 2. let that be your working directory in R. This means that getwd() should say C:/Users/nwayyin/AromaAnalysis This is not what you did either ! Please make sure that you did what has been suggested. Thanks, Pierre On Wed, May 1, 2013 at 2:27 PM, nawin MOHAMMED naw...@gmail.comjavascript: wrote: getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 chipType - HG-U133_Plus_2 chipTypeS - gsub(,.*, , chipType) path - Arguments$getReadablePath(chipTypeS, path=pathAC, mustExist=TRUE) Error in getReadablePath.Arguments(static, ...) : object 'pathAC' not found On Wednesday, May 1, 2013 1:22:08 PM UTC+1, nawin MOHAMMED wrote: I also tried put the cdf file in the HG-U133_Plus_2 folder directly as u see in the path but same error pathAC - Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 13:20:42] Exception: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' getwd() [1] C:/Users/nawin/AromaAnalysis/HG-U133_Plus_2 On Wednesday, May 1, 2013 1:13:18 PM UTC+1, nawin MOHAMMED wrote: Hi Henrik i changed the directory as you told me but i got this error ?? ' pathAC - Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 13:11:50] Exception: Pathname not found: AromaAnalysis/ChipType/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/ChipType/] exist; current directory is 'C:/Users/nawin/AromaAnalysis/ChipType/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/ChipType/HG-U133_Plus_2,
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
hi henrik , please i can understand what is the problem ??? iam using R3 with 64X and i try what you tolde me also i call for list file as bellow pathAC - Arguments$getReadablePath(annotationData/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 15:32:56] Exception: Pathname not found: annotationData/HG-U133_Plus_2 (none of the parent directories [annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(annotationData/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: annotationData/HG-U133_Plus_2 (none of the parent directories [annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' library(R.utils) pathAC - Arguments$getReadablePath(AromaAnalysis/annotationData/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 16:06:11] Exception: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/annotationData/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' * list.files()* *[1] HG-U133_Plus_2.cdf* On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote: Hi. On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED naw...@gmail.comjavascript: wrote: hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma : Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type chipType in a directory of format: annotationData/chipTypes/chip type/ and my location is C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 i just creat new folder in annotation data with name chip type and inside it another folder with chip name ??? iam just confused ?? What you're missing in Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory is the part that says ***of the current working directory***. In other words, in your current working directory (i.e. getwd()) you should see subdirectory annotationData if you call list.files(). You may find the following page useful too: http://aroma-project.org/troubleshooting/DirectoryStructures Also, I strongly recommend to put your data files (annotationData/, rawData/, etc.) somewhere else than where R installs packages. Right now you seem to place them in: C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 The directory 'C:/Users/nwayyin/Documents/R/win-library/3.0/' is where R install packages and you shouldn't add/remove things from there. For instance, if you uninstall
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
Dear Narwin, please see the message that I've sent you offline and continue any correspondence there instead of here. /Henrik On Wed, May 1, 2013 at 8:17 AM, nawin MOHAMMED nawi...@gmail.com wrote: hi henrik , please i can understand what is the problem ??? iam using R3 with 64X and i try what you tolde me also i call for list file as bellow pathAC - Arguments$getReadablePath(annotationData/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 15:32:56] Exception: Pathname not found: annotationData/HG-U133_Plus_2 (none of the parent directories [annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(annotationData/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: annotationData/HG-U133_Plus_2 (none of the parent directories [annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' library(R.utils) pathAC - Arguments$getReadablePath(AromaAnalysis/annotationData/HG-U133_Plus_2, mustExist=TRUE) [2013-05-01 16:06:11] Exception: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') at #05. getReadablePathname.Arguments(static, path = path, mustExist = mustExist, ...) - getReadablePathname.Arguments() is in environment 'R.utils' at #04. getReadablePathname(static, path = path, mustExist = mustExist, ...) - getReadablePathname() is in environment 'R.utils' at #03. getReadablePath.Arguments(static, ...) - getReadablePath.Arguments() is in environment 'R.utils' at #02. getReadablePath(static, ...) - getReadablePath() is in environment 'R.utils' - originating from 'text' at #01. Arguments$getReadablePath(AromaAnalysis/annotationData/HG-U133_Plus_2, mustExist = TRUE) - Arguments$getReadablePath() is local of the calling function Error: Pathname not found: AromaAnalysis/annotationData/HG-U133_Plus_2 (none of the parent directories [AromaAnalysis/annotationData/] exist; current directory is 'C:/Users/nwayyin/AromaAnalysis/annotationData/HG-U133_Plus_2') In addition: Warning messages: 1: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' 2: In is.na(parent) : is.na() applied to non-(list or vector) of type 'NULL' list.files() [1] HG-U133_Plus_2.cdf On Tuesday, April 30, 2013 5:02:48 PM UTC+1, Henrik Bengtsson wrote: Hi. On Tue, Apr 30, 2013 at 8:26 AM, nawin MOHAMMED naw...@gmail.com wrote: hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma : Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type chipType in a directory of format: annotationData/chipTypes/chip type/ and my location is C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 i just creat new folder in annotation data with name chip type and inside it another folder with chip name ??? iam just confused ?? What you're missing in Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory is the part that says ***of the current working directory***. In other words, in your current working directory (i.e. getwd()) you should see subdirectory annotationData if you call list.files(). You may find the following page useful too: http://aroma-project.org/troubleshooting/DirectoryStructures Also, I strongly recommend to put your data files (annotationData/, rawData/, etc.) somewhere else than where R installs packages. Right now you seem to place them in: C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 The
[aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
thank you very much for your advice but i was typing fast so i did not saw these false world , any way ia still complaining from the same problem , please can you explain to me where is the error in the code you can check the path in the code that what i was trying to explian is there is some thing wrong with path ??? or where is the problem is ?? On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote: Hi, Please create a new thread (with a relevant subject line) instead of replying to an unrelated one. See below. On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED naw...@gmail.comjavascript: wrote: Greeting , iam a Phd student , i try implement aroma package but its not working with me , i don't know where is the error, and i have question the shiptype folder is not exist be default in annotationdata, i just create a folder in annotation data name it chiptype and i put the cdf file in it , is that possible ??? please i need your advice this is my program Yes, that's what you should do. Here is some general advice that could save you lots of time: 1. Read carefully the setup page: http://www.aroma-project.org/setup, and follow the links in that page. 2. Be really careful with the folder and file names: annotationData is not the same as annotationdata, etc. The same holds for function names in the code you have pasted below, for example AffymetrixcdfFile is not the same as AffymetrixCdfFile, etc... 3. Do not try to guess/invent code lines if you are not familiar with the aroma framework. Instead, try to reproduce a vignette, for example this one: http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis Best, Pierre getwd() [1] C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType ChipType(HG-U133_Plus_2) Error: unexpected symbol in ChipType(HG ChipType(HG-U133_Plus_2) Error: could not find function ChipType chipType(HG-U133_Plus_2) Error: could not find function chipType library(aroma.affymetrix) ChipeType(HG-U133_Plus_2) Error: could not find function ChipeType chipType-HG-U133_Plus_2 cdf-AffymetrixcdfFile$byChipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-AffymetrixcdfFile$bychipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-AffymetrixcdfFile$byChipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-HG-U133_Plus_2$bychipType(HG-U133_Plus_2) Error: object 'HG' not found cdf-AffymetrixcdfFile$bychipType(HG-U133_Plus_2, tags=ChipType) Error: object 'AffymetrixcdfFile' not found the error is with cdf file which can not be read i download all the package source(http://bioconductor.org/biocLite.R;) biocLite(biomaRt) hbInstall(aroma.affymetrix) thank you -- -- 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.
Re: [aroma.affymetrix] Re: Setting up annotation data in aroma.affymetrix
hi Pierre, the anootationData is allocated by default in the aroma.affymetrix ?? is it ??? as its declare in the page of aroma : Aroma.affymetrix searches for CDF files in the annotationData/ directory of the current working directory. Place the CDF for chip type chipType in a directory of format: annotationData/chipTypes/chip type/ and my location is C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/HG-U133_Plus_2 i just creat new folder in annotation data with name chip type and inside it another folder with chip name ??? iam just confused ?? why this error occur please if you know the cause of problem please tell me On Tuesday, April 30, 2013 3:16:00 PM UTC+1, Pierre Neuvial wrote: Hi, Quoting myself, 1. Read carefully the setup page: http://www.aroma-project.org/setup, and follow the links in that page. The first link Location of annotation data files explains where annotation data files should be located. Best, Pierre On Tue, Apr 30, 2013 at 2:10 PM, nawin MOHAMMED naw...@gmail.comjavascript: wrote: i also down load the CDF from affymetrix but its not working same problem Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and with filename extension 'cdf'. cdf - AffymetrixCdfFile$byChipType(HG-U133_Plus_2,tags=full) [2013-04-30 13:08:07] Exception: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and with filename extension 'cdf'. at #03. byChipType.UnitAnnotationDataFile(static, ...) - byChipType.UnitAnnotationDataFile() is in environment 'aroma.core' at #02. byChipType(static, ...) - byChipType() is in environment 'aroma.core' - originating from 'text' at #01. AffymetrixCdfFile$byChipType(HG-U133_Plus_2, tags = full) - AffymetrixCdfFile$byChipType() is local of the calling function Error: Failed to create AffymetrixCdfFile object. Could not locate an annotation data file for chip type 'HG-U133_Plus_2' with tags 'full' and with filename extension 'cdf'. getwd() [1] C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/chipType/CD_hgu133a2_libraryfile On Tuesday, April 30, 2013 8:40:35 AM UTC+1, Pierre Neuvial wrote: Hi, Please create a new thread (with a relevant subject line) instead of replying to an unrelated one. See below. On Tue, Apr 30, 2013 at 9:22 AM, nawin MOHAMMED naw...@gmail.com wrote: Greeting , iam a Phd student , i try implement aroma package but its not working with me , i don't know where is the error, and i have question the shiptype folder is not exist be default in annotationdata, i just create a folder in annotation data name it chiptype and i put the cdf file in it , is that possible ??? please i need your advice this is my program Yes, that's what you should do. Here is some general advice that could save you lots of time: 1. Read carefully the setup page: http://www.aroma-project.org/setup, and follow the links in that page. 2. Be really careful with the folder and file names: annotationData is not the same as annotationdata, etc. The same holds for function names in the code you have pasted below, for example AffymetrixcdfFile is not the same as AffymetrixCdfFile, etc... 3. Do not try to guess/invent code lines if you are not familiar with the aroma framework. Instead, try to reproduce a vignette, for example this one: http://www.aroma-project.org/vignettes/GeneSTArrayAnalysis Best, Pierre getwd() [1] C:/Users/nwayyin/Documents/R/win-library/3.0/aroma.affymetrix/annotationData/ChipType ChipType(HG-U133_Plus_2) Error: unexpected symbol in ChipType(HG ChipType(HG-U133_Plus_2) Error: could not find function ChipType chipType(HG-U133_Plus_2) Error: could not find function chipType library(aroma.affymetrix) ChipeType(HG-U133_Plus_2) Error: could not find function ChipeType chipType-HG-U133_Plus_2 cdf-AffymetrixcdfFile$byChipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-AffymetrixcdfFile$bychipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-AffymetrixcdfFile$byChipType(HG-U133_Plus_2) Error: object 'AffymetrixcdfFile' not found cdf-HG-U133_Plus_2$bychipType(HG-U133_Plus_2) Error: object 'HG' not found cdf-AffymetrixcdfFile$bychipType(HG-U133_Plus_2, tags=ChipType) Error: object 'AffymetrixcdfFile' not found the error is with cdf file which can not be read i download all the package
