Thanks. This helped me resolve the issue. Nitesh
On Monday, 18 June 2012 17:19:27 UTC-4, Henrik Bengtsson wrote: > > On Mon, Jun 18, 2012 at 1:59 PM, NT_CMU <[email protected]> wrote: > > Hi > > > > Thanks for the help Pierre. I managed to resolve it. I am just using the > > AffymetrixCelSet$byName with the cdf information instead of the > chipType. > > For some reason, that still refuses to work. > > These are the two possible ways to setup the CEL data set: > > cs <- AffymetrixCelSet$byName("LeeAV_2012", > chipType="GenomeWideSNP_6,Full") > > and > > cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full"); > cs <- AffymetrixCelSet$byName("LeeAV_2012", cdf=cdf); > > and it appears from you file listing that that should be the case for > you. If you get both to work, you've ready to move on. > > /Henrik > > > > > Nitesh > > > > > > On Monday, 18 June 2012 11:39:34 UTC-4, NT_CMU 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") > >> 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. > >> > >> 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/
