edgeR query
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Shravanthi P ▴ 20
@shravanthi-p-5482
Last seen 7.4 years ago
I am new to using R and my project is on differential gene expression .I was told to use Edger but I am having trouble reading a tab delimited format data for affy oligonucleotide microarray data . How can I read the data into R ? and how can I identify the upregulated and downregulated genes ? [[alternative HTML version deleted]]
Microarray affy edgeR Microarray affy edgeR • 1.0k views
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@steve-lianoglou-2771
Last seen 1 day ago
United States
Hi Shravanthi, On Tue, Sep 4, 2012 at 6:33 AM, Shravanthi P <shravanthipsg at="" gmail.com=""> wrote: > I am new to using R and my project is on differential gene expression .I > was told to use Edger but I am having trouble reading a tab delimited > format data for affy oligonucleotide microarray data . > How can I read the data into R ? and how can I identify the upregulated and > downregulated genes ? The bad news is that you've got a long way to go before you can get from where you are to where you want to be. The good news is that there are a lot of resources available for your self study that can help you get to where you want to be. It would be in your best interest to learn more about R first (start with an intro to R) before you try to do anything more serious. After you do that, and you then read the (very helpful) edgeR user manual (as Wenhuo already suggested) -- you'll probably come to the realization that edgeR is the wrong tool for this job. You have microarray data and edgeR is used for sequencing data. In this case, you'll find that the limma package is probably what you're after. Fortunately for you, there is a very thorough limma user guide that you can read through that gives you some idea of how to process different types of microarray data. The goods at the link below (and the associated packages) are worth some study as well: http://bioconductor.org/help/workflows/oligo-arrays/ HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Thanks a lot for correcting my error. I have downloaded the Limma package(it seems to be majorly for spotted microarray as opposed to oligonucleotides microarry). I am having trouble even reading my data into R. I have the tab delimited format file for a series (eg GSE9936) .How do I read and initialize it to an object in R? And how to I define groups within this file for a comparison.Limma user manual directed me to use the affy package for normalizing data.Can I not use the already available normalized data ? I have a time constraint and was hoping to avoid this step. My aim is to find the up regulated and downregulated genes in breast cancer cells when treated with Genistein on a time progression basis (with a constant concentration) On 9/5/12, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi Shravanthi, > > On Tue, Sep 4, 2012 at 6:33 AM, Shravanthi P <shravanthipsg at="" gmail.com=""> > wrote: >> I am new to using R and my project is on differential gene expression .I >> was told to use Edger but I am having trouble reading a tab delimited >> format data for affy oligonucleotide microarray data . >> How can I read the data into R ? and how can I identify the upregulated >> and >> downregulated genes ? > > The bad news is that you've got a long way to go before you can get > from where you are to where you want to be. The good news is that > there are a lot of resources available for your self study that can > help you get to where you want to be. > > It would be in your best interest to learn more about R first (start > with an intro to R) before you try to do anything more serious. > > After you do that, and you then read the (very helpful) edgeR user > manual (as Wenhuo already suggested) -- you'll probably come to the > realization that edgeR is the wrong tool for this job. You have > microarray data and edgeR is used for sequencing data. > > In this case, you'll find that the limma package is probably what > you're after. Fortunately for you, there is a very thorough limma user > guide that you can read through that gives you some idea of how to > process different types of microarray data. The goods at the link > below (and the associated packages) are worth some study as well: > > http://bioconductor.org/help/workflows/oligo-arrays/ > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact >
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Hi Shravanthi, > library(GEOquery) > dat <- getGEO("GSE9936")[[1]] > dat ExpressionSet (storageMode: lockedEnvironment) assayData: 22283 features, 105 samples element names: exprs protocolData: none phenoData sampleNames: GSM251354 GSM251355 ... GSM251458 (105 total) varLabels: title geo_accession ... data_row_count (37 total) varMetadata: labelDescription featureData featureNames: 1007_s_at 1053_at ... AFFX-TrpnX-M_at (22283 total) fvarLabels: ID GB_ACC ... Gene Ontology Molecular Function (16 total) fvarMetadata: Column Description labelDescription experimentData: use 'experimentData(object)' Annotation: GPL96 > table(pData(phenoData(dat))[,11]) treated with 300nM genistein 17 treated with 300nM genistein and 3uM ICI182,780 13 treated with 300nM S-Equol 13 treated with 300nM S-Equol and 3uM ICI 182,780 9 treated with 6nM 17beta-estradiol 14 treated with 6nM genistein 18 treated with vehicle control 21 Note that the limma package is quite happy to use an ExpressionSet as input, and the 11th column of the phenoData slot contains the treatment. That should get you well on your way. You should at the very least read the majority of the limma User's Guide. Best, Jim On 9/5/2012 8:16 AM, Shravanthi P wrote: > Thanks a lot for correcting my error. I have downloaded the Limma > package(it seems to be majorly for spotted microarray as opposed to > oligonucleotides microarry). I am having trouble even reading my data > into R. I have the tab delimited format file for a series (eg GSE9936) > .How do I read and initialize it to an object in R? And how to I > define groups within this file for a comparison.Limma user manual > directed me to use the affy package for normalizing data.Can I not use > the already available normalized data ? > I have a time constraint and was hoping to avoid this step. > > My aim is to find the up regulated and downregulated genes in breast > cancer cells when treated with Genistein on a time progression basis > (with a constant concentration) > > On 9/5/12, Steve Lianoglou<mailinglist.honeypot at="" gmail.com=""> wrote: >> Hi Shravanthi, >> >> On Tue, Sep 4, 2012 at 6:33 AM, Shravanthi P<shravanthipsg at="" gmail.com=""> >> wrote: >>> I am new to using R and my project is on differential gene expression .I >>> was told to use Edger but I am having trouble reading a tab delimited >>> format data for affy oligonucleotide microarray data . >>> How can I read the data into R ? and how can I identify the upregulated >>> and >>> downregulated genes ? >> The bad news is that you've got a long way to go before you can get >> from where you are to where you want to be. The good news is that >> there are a lot of resources available for your self study that can >> help you get to where you want to be. >> >> It would be in your best interest to learn more about R first (start >> with an intro to R) before you try to do anything more serious. >> >> After you do that, and you then read the (very helpful) edgeR user >> manual (as Wenhuo already suggested) -- you'll probably come to the >> realization that edgeR is the wrong tool for this job. You have >> microarray data and edgeR is used for sequencing data. >> >> In this case, you'll find that the limma package is probably what >> you're after. Fortunately for you, there is a very thorough limma user >> guide that you can read through that gives you some idea of how to >> process different types of microarray data. The goods at the link >> below (and the associated packages) are worth some study as well: >> >> http://bioconductor.org/help/workflows/oligo-arrays/ >> >> HTH, >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> | Memorial Sloan-Kettering Cancer Center >> | Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> > _______________________________________________ > 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
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Alyaa Mahmoud ▴ 440
@alyaa-mahmoud-4670
Last seen 22 months ago
read.table or read.delim there are many ways to determine up/down regulated genes, are u asking about the commands in edgeR in particular ? Alyaa On Tue, Sep 4, 2012 at 1:33 PM, Shravanthi P <shravanthipsg@gmail.com>wrote: > I am new to using R and my project is on differential gene expression .I > was told to use Edger but I am having trouble reading a tab delimited > format data for affy oligonucleotide microarray data . > How can I read the data into R ? and how can I identify the upregulated and > downregulated genes ? > > [[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 > -- Alyaa Mahmoud "Love all, trust a few, do wrong to none"- Shakespeare [[alternative HTML version deleted]]
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Hi Shravanthi <https: plus.google.com="" u="" 0="" 111065650556993784508?prsrc="4">, I suggest you read through the edgeR manual. If you are new to R, then you probably need to read through the R manual. Best, Wenhuo On Tue, Sep 4, 2012 at 7:39 AM, Alyaa Mahmoud <alyamahmoud@gmail.com> wrote: > read.table or read.delim > > there are many ways to determine up/down regulated genes, are u asking > about the commands in edgeR in particular ? > > Alyaa > > On Tue, Sep 4, 2012 at 1:33 PM, Shravanthi P <shravanthipsg@gmail.com> >wrote: > > > I am new to using R and my project is on differential gene expression .I > > was told to use Edger but I am having trouble reading a tab delimited > > format data for affy oligonucleotide microarray data . > > How can I read the data into R ? and how can I identify the upregulated > and > > downregulated genes ? > > > > [[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 > > > > > > -- > Alyaa Mahmoud > > "Love all, trust a few, do wrong to none"- Shakespeare > > [[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 > -- Wenhuo Hu Park lab Memorial Sloan Kettering Cancer Center Zuckerman Research Building 408 East 69th Street Room ZRC-527 New York, NY 10065 Phone 646-888-3220 huw@mskcc.org [[alternative HTML version deleted]]
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