Hi Pierre, Thanks for the reply. My file structure is :
Nitesh-MacPro:Affy6.0 niteshturaga$ ls -R | grep ":$" | sed -e 's/:$//' -e 's/[^-][^\/]*\//--/g' -e 's/^/ /' -e 's/-/|/' * * *|-Affy6.0* |-Text-Export *|-annotationData* |---chipTypes |-----GenomeWideSNP_6 |---------GenomeWideSNP_6,Full.CDF * |-rawData* |---DATfiles |---GRDfiles |---LeeAV_2012 |-----GenomeWideSNP_6 |---------LeePosCon-120911-GenomeWideSNP-62.CEL |---------11-0504-re-GenomeWideSNP-62.CEL There are more .CEL in the LeeAV_2012/GenomewideSNP_6 folder but i listed only 2. Thanks Nitesh On Monday, 18 June 2012 12:34:30 UTC-4, Pierre Neuvial wrote: > > Hi, > > On Mon, Jun 18, 2012 at 5:39 PM, NT_CMU <[email protected]> wrote: > > Hi > > > > I am new to aroma.affymetrix. I am not sure why the command > > "AffymetrixCelSet$byName" is not working. > > > > cs <- AffymetrixCelSet$byName("test.CEL",chipType = > > "../../annotationData/chipTypes/GenomeWideSNP_6") > > This will not work because > 1- the first argument of 'AffymetrixCelSet$byName' should be the name > of your data set (this is why this function is called "byName"), as it > appears in your "rawData" folder. Is should not be a file name as > "test.CEL" > 2- the 'chipType' argument should really be a chip type, e.g. > "GenomeWideSNP_6", not a path to a cdf file (as > "../../annotationData/chipTypes/GenomeWideSNP_6" is). > > More below. > > > Error in method(static, ...) : > > [2012-06-18 11:34:57] Exception: Failed to create AffymetrixCdfFile > object. > > Could to locate an annotation data file for chip type > > '../../annotationData/chipTypes/GenomeWideSNP_6' (without requiring any > > tags) and with filename extension 'cdf'. > > > > at #04. method(static, ...) > > - method() is in environment 'aroma.core' > > > > at #03. AffymetrixCdfFile$byChipType(chipType) > > - AffymetrixCdfFile$byChipType() is local of the calling > function > > > > at #02. method(static, ...) > > - method() is in environment 'aroma.affymetrix' > > > > at #01. AffymetrixCelSet$byName("test.CEL", chipType = > > "../../annotationData/chipTypes/GenomeWideSNP_6") > > - AffymetrixCelSet$byName() is local of the calling function > > > > > > I think my directory structure is wrong. But i could use some pointers > on > > how to get things moving because i've been trying to get this command > > working for over 4 days now. > > I don't know what your file structure is, can you describe it ? > Your file structure should match this one: > > http://aroma-project.org/setup/QuickSummaryOfRequiredFileStructure > > When you have that, you should be able to define an AffymetrixCelSet using > "AffymetrixCelSet$byName", for example > > cs <- AffymetrixCelSet$byName("myDataSet",chipType="GenomeWideSNP_6") > > where "myDataSet" is a character string containing the name of your > data set (not file names), and "GenomeWideSNP_6" is your chip type. > > Important note: you should make sure that the working directory of > your R session contains "annotationData", "rawData", etc. > Is that the case for you ? > > Cheers, > > Pierre > > PS (quoting Henrik): "If you find yourself specifying paths or full > pathname in your main > aroma.affymetrix scripts, you are doing something wrong. The package > is design to work without having to specify paths. A rule of thumb is > that you should be able to move any aroma.affymetrix script to another > computer system and run it without having to change anything." [thread > 'How do you analyze Gene ST Data?', Oct 21, 2008]. > > > > > Also, another issue is I am able to load CDF files with the basic > > "AffymetrixCdfFile("GenomeWideSNP_6,Full.CDF") ". But if i use the > command > > AffymetrixCdfFile$byChipType("GenomeWideSNP_6",tags="Full"), it gives me > an > > error. Am I doing something really wrong? > > > > Thanks > > > > Nitesh > > > > > > -- > > 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 [email protected] > > 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 [email protected] To unsubscribe and other options, go to http://www.aroma-project.org/forum/
