Question: annotation of affymetrix microarray data
0
gravatar for Taylor, Katie
9.6 years ago by
Taylor, Katie90 wrote:
Dear Sir/Madam, I hope that this email finds you well. I am currently undertaking a PhD and I have performed some arrays on the illumina platforms. I have also downloaded some affymetrix data from GEO (GDS2609) which I have successfully analysed in bioconductor. I am new to bioconductor however and so I rely heavily on the worked examples given in the pdf documentation at bioconductor. I recently tried to use the annaffy package to annotate the data but I was unsuccessful. I have tried to use the script that is given as an example in the annaffy pdf but it won't work on my data set. I am sure that it is probably something that I am doing wrong. Instead of entering > data(aafExpr) I entered: > data(GDS2609) as this is the name of the file that I want to open. I can get individual symbols but not a list or table. I tried emailing the person who wrote the annaffy pdf but he advised me to email the bioconductor emailing list - I hope I am emailing the correct place. If you could give me any advice I would be really grateful. I am trying to annotate the GDS2609 dataset and I'm hoping that you will be able to help me. I appreciate any help that you can offer me. Thank you and best wishes, Katie
annotate annaffy • 550 views
ADD COMMENTlink modified 9.6 years ago by Sean Davis21k • written 9.6 years ago by Taylor, Katie90
Answer: annotation of affymetrix microarray data
0
gravatar for Sean Davis
9.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Apr 27, 2010 at 6:28 AM, Taylor, Katie <kt70 at="" leicester.ac.uk=""> wrote: > Dear Sir/Madam, > > I hope that this email finds you well. I am currently undertaking a PhD and I have performed some arrays on the illumina platforms. I have also downloaded some affymetrix data from GEO (GDS2609) which I have successfully analysed in bioconductor. I am new to bioconductor however and so I rely heavily on the worked examples given in the pdf documentation at bioconductor. I recently tried to use the annaffy package to annotate the data but I was unsuccessful. I have tried to use the script that is given as an example in the annaffy pdf but it won't work on my data set. I am sure that it is probably something that I am doing wrong. Instead of entering > >> data(aafExpr) > > I entered: > >> data(GDS2609) > > as this is the name of the file that I want to open. I can get individual symbols but not a list or table. I tried emailing the person who wrote the annaffy pdf but he advised me to email the bioconductor emailing list - I hope I am emailing the correct place. If you could give me any advice I would be really grateful. I am trying to annotate the GDS2609 dataset and I'm hoping that you will be able to help me. I appreciate any help that you can offer me. > Hi, Katie. The data set is already annotated by NCBI GEO and Affymetrix. Try the following: library(GEOquery) gds <- GDS2eSet(getGEO('GDS2609')) head(fData(gds)) varLabels(featureData(gds)) Also, it is worth noting that this GDS was run on the hgu133plus2 array, so you can also access the bioconductor annotation package that matches, if you like. Sean
ADD COMMENTlink written 9.6 years ago by Sean Davis21k
Answer: annotation of affymetrix microarray data
0
gravatar for Wolfgang Huber
9.6 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Dear Katie from the way you phrase your question I presume you have not yet had the chance to familiarise yourself with the basics of R programming? If so, doing that would be a good starting point. It's worth the effort. Without, you will not have much fun with Bioconductor. With a basic knowledge of R, I am sure the examples in the vignettes (and in fact, many other things in life) will start making more sense to you, and, importantly, you will be able to modify the workflows explained in the vignettes to match exactly your needs. Best wishes Wolfgang Taylor, Katie ha scritto: > Dear Sir/Madam, > > I hope that this email finds you well. I am currently undertaking a PhD and I have performed some arrays on the illumina platforms. I have also downloaded some affymetrix data from GEO (GDS2609) which I have successfully analysed in bioconductor. I am new to bioconductor however and so I rely heavily on the worked examples given in the pdf documentation at bioconductor. I recently tried to use the annaffy package to annotate the data but I was unsuccessful. I have tried to use the script that is given as an example in the annaffy pdf but it won't work on my data set. I am sure that it is probably something that I am doing wrong. Instead of entering > >> data(aafExpr) > > I entered: > >> data(GDS2609) > > as this is the name of the file that I want to open. I can get individual symbols but not a list or table. I tried emailing the person who wrote the annaffy pdf but he advised me to email the bioconductor emailing list - I hope I am emailing the correct place. If you could give me any advice I would be really grateful. I am trying to annotate the GDS2609 dataset and I'm hoping that you will be able to help me. I appreciate any help that you can offer me. > > Thank you and best wishes, > > Katie > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
ADD COMMENTlink written 9.6 years ago by Wolfgang Huber13k
Absolutely true And the manual by Dr. Girke at <http: manuals.bioinformatics.ucr.edu="" home="" r_biocondmanual=""> is very helpful for novices (me) > From: Wolfgang Huber <whuber at="" embl.de=""> > Date: Tue, 27 Apr 2010 20:58:22 +0200 > To: "Taylor, Katie" <kt70 at="" leicester.ac.uk=""> > Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: Re: [BioC] annotation of affymetrix microarray data > > > Dear Katie > > from the way you phrase your question I presume you have not yet had the > chance to familiarise yourself with the basics of R programming? > > If so, doing that would be a good starting point. It's worth the effort. > Without, you will not have much fun with Bioconductor. With a basic > knowledge of R, I am sure the examples in the vignettes (and in fact, > many other things in life) will start making more sense to you, and, > importantly, you will be able to modify the workflows explained in the > vignettes to match exactly your needs. > > Best wishes > Wolfgang > > > Taylor, Katie ha scritto: >> Dear Sir/Madam, >> >> I hope that this email finds you well. I am currently undertaking a PhD and I >> have performed some arrays on the illumina platforms. I have also downloaded >> some affymetrix data from GEO (GDS2609) which I have successfully analysed in >> bioconductor. I am new to bioconductor however and so I rely heavily on the >> worked examples given in the pdf documentation at bioconductor. I recently >> tried to use the annaffy package to annotate the data but I was unsuccessful. >> I have tried to use the script that is given as an example in the annaffy pdf >> but it won't work on my data set. I am sure that it is probably something >> that I am doing wrong. Instead of entering >> >>> data(aafExpr) >> >> I entered: >> >>> data(GDS2609) >> >> as this is the name of the file that I want to open. I can get individual >> symbols but not a list or table. I tried emailing the person who wrote the >> annaffy pdf but he advised me to email the bioconductor emailing list - I >> hope I am emailing the correct place. If you could give me any advice I would >> be really grateful. I am trying to annotate the GDS2609 dataset and I'm >> hoping that you will be able to help me. I appreciate any help that you can >> offer me. >> >> Thank you and best wishes, >> >> Katie >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 9.6 years ago by Loren Engrav1.0k
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