Question: Regarding CDF file
0
gravatar for deepika lakhwani
6.5 years ago by
deepika lakhwani170 wrote:
Dear Sir, I have arabidopsis cel files and for differential expression analysis, i am using AffylmGUI package but its not running because AraGene-1_0-st CDF file is not available on http://www.bioconductor.org/data/metaData.html site and when i downloaded the data from affymetrix site, there are so many files such as PGF, CLF, QCC files in it but no CDF files. what should i do ? Please suggest me. Can you upload the AraGene-1_0-st CDF file or is there any other solution for it. ThankingYou regards Deepika [[alternative HTML version deleted]]
cdf affylmgui • 756 views
ADD COMMENTlink modified 6.5 years ago by James W. MacDonald51k • written 6.5 years ago by deepika lakhwani170
Answer: Regarding CDF file
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gravatar for James W. MacDonald
6.5 years ago by
United States
James W. MacDonald51k wrote:
Hi Deepika, On 5/28/2013 9:58 AM, deepika lakhwani wrote: > Dear Sir, > > I have arabidopsis cel files and for differential expression analysis, i am > using AffylmGUI package but its not running because AraGene-1_0-st CDF file > is not available on http://www.bioconductor.org/data/metaData.html site and > when i downloaded the data from affymetrix site, there are so many files > such as PGF, CLF, QCC files in it but no CDF files. what should i do ? > Please suggest me. Can you upload the AraGene-1_0-st CDF file or is there > any other solution for it. You should be processing these arrays using either oligo or xps. If you use oligo, the correct file will automatically be downloaded for you. Best, Jim > > > ThankingYou > > > > regards > Deepika > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.5 years ago by James W. MacDonald51k
Answer: Regarding CDF file
0
gravatar for Fiona
6.5 years ago by
Fiona70
United Kingdom
Fiona70 wrote:
Dear Deepika, I had a similar problem when using Affy microRNA arrays. I emailed Affymetrix support at supporteurope@affymetrix.com although note that there are different email addresses depending on where you are based - the information is all on their website (http://www.affymetrix.com/about_affymetrix/contact_us/index.affx). Anyway, they very quickly were able to give me access to the .cdf file I needed. Hope this helps, Fiona Dr Fiona C Ingleby Postdoctoral Research Fellow University of Sussex Website: fionaingleby.weebly.com On 28 May 2013, at 14:58, deepika lakhwani <lakhwanideepika@gmail.com> wrote: > Dear Sir, > > I have arabidopsis cel files and for differential expression analysis, i am > using AffylmGUI package but its not running because AraGene-1_0-st CDF file > is not available on http://www.bioconductor.org/data/metaData.html site and > when i downloaded the data from affymetrix site, there are so many files > such as PGF, CLF, QCC files in it but no CDF files. what should i do ? > Please suggest me. Can you upload the AraGene-1_0-st CDF file or is there > any other solution for it. > > > ThankingYou > > > > regards > Deepika > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]
ADD COMMENTlink written 6.5 years ago by Fiona70
Answer: Regarding CDF file
0
gravatar for James W. MacDonald
6.5 years ago by
United States
James W. MacDonald51k wrote:
Hi Deepika, Please don't take things off-list (e.g., use reply-all when responding). On 5/29/2013 12:11 AM, deepika lakhwani wrote: > Thanks for your advice.. > I am using R 2.15 version so xps is not working on it. Suggest me xps > is better than oligo or not. I don't know if xps is better than oligo or not. I suspect they are roughly comparable, although I have no experience with xps other than trying to install it back when installing ROOT on Windows was more difficult than it appears to be these days. I will say that xps has been around for a long time, and most certainly can be installed using R-2.15. You do need to install ROOT first. See the README that comes with the package: http://bioconductor.org/packages/release/bioc/readmes/xps/README Best, Jim > > > On Tue, May 28, 2013 at 8:59 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Deepika, > > > On 5/28/2013 9:58 AM, deepika lakhwani wrote: > > Dear Sir, > > I have arabidopsis cel files and for differential expression > analysis, i am > using AffylmGUI package but its not running because > AraGene-1_0-st CDF file > is not available on > http://www.bioconductor.org/data/metaData.html site and > when i downloaded the data from affymetrix site, there are so > many files > such as PGF, CLF, QCC files in it but no CDF files. what > should i do ? > Please suggest me. Can you upload the AraGene-1_0-st CDF file > or is there > any other solution for it. > > > You should be processing these arrays using either oligo or xps. > If you use oligo, the correct file will automatically be > downloaded for you. > > Best, > > Jim > > > > > > > ThankingYou > > > > regards > Deepika > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > regards > deepika -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.5 years ago by James W. MacDonald51k
Dear Deepika, As Jim kindly mentioned, for xps you need to install ROOT first. Could you please show your sessionInfo() so that I know which OS you are using, so that I can tell you which version of ROOT to install. Best regards, Christian _._._._._._._._._._._._._._._._._._ C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a V.i.e.n.n.a A.u.s.t.r.i.a e.m.a.i.l: cstrato at aon.at _._._._._._._._._._._._._._._._._._ On 5/29/13 4:16 PM, James W. MacDonald wrote: > Hi Deepika, > > Please don't take things off-list (e.g., use reply-all when responding). > > On 5/29/2013 12:11 AM, deepika lakhwani wrote: >> Thanks for your advice.. >> I am using R 2.15 version so xps is not working on it. Suggest me xps >> is better than oligo or not. > > I don't know if xps is better than oligo or not. I suspect they are > roughly comparable, although I have no experience with xps other than > trying to install it back when installing ROOT on Windows was more > difficult than it appears to be these days. I will say that xps has been > around for a long time, and most certainly can be installed using R-2.15. > > You do need to install ROOT first. See the README that comes with the > package: > > http://bioconductor.org/packages/release/bioc/readmes/xps/README > > Best, > > Jim > > >> >> >> On Tue, May 28, 2013 at 8:59 PM, James W. MacDonald <jmacdon at="" uw.edu="">> <mailto:jmacdon at="" uw.edu="">> wrote: >> >> Hi Deepika, >> >> >> On 5/28/2013 9:58 AM, deepika lakhwani wrote: >> >> Dear Sir, >> >> I have arabidopsis cel files and for differential expression >> analysis, i am >> using AffylmGUI package but its not running because >> AraGene-1_0-st CDF file >> is not available on >> http://www.bioconductor.org/data/metaData.html site and >> when i downloaded the data from affymetrix site, there are so >> many files >> such as PGF, CLF, QCC files in it but no CDF files. what >> should i do ? >> Please suggest me. Can you upload the AraGene-1_0-st CDF file >> or is there >> any other solution for it. >> >> >> You should be processing these arrays using either oligo or xps. >> If you use oligo, the correct file will automatically be >> downloaded for you. >> >> Best, >> >> Jim >> >> >> >> >> >> >> ThankingYou >> >> >> >> regards >> Deepika >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> >> regards >> deepika >
ADD REPLYlink written 6.5 years ago by cstrato3.9k
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