Working with Agilent 4X44k array,two color experiment

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Srikanth Manda Srinivas ▴ 200

@srikanth-manda-srinivas-4590

Last seen 10.3 years ago

Hi Everyone, I would like to know if we have specific package to work with Agilent 4X44k array just like Affy. Please guide me how one go for generating HeatMaps and other analysis on this data. I am a newbie in this area. Regards, -- Srikanth Manda Srinivas Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+917259692031 [[alternative HTML version deleted]]

GO affy GO affy • 1.9k views

ADD COMMENT • link updated 13.5 years ago by Srinivas Srikanth ▴ 70 • written 13.5 years ago by Srikanth Manda Srinivas ▴ 200

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Sean Davis 21k

@sean-davis-490

Last seen 4 months ago

United States

On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas <srikanth at="" ibioinformatics.org=""> wrote: > Hi Everyone, > > I would like to know if we have specific package to work with Agilent 4X44k > array just like Affy. Please guide me how one go for generating HeatMaps and > other analysis on this data. I am a newbie in this area. Take a look at the Agi4x44Preprocess package. If you are new to microarray data analysis using bioconductor, take a look at the limma package and its documentation, particularly the user guide. Sean

ADD COMMENT • link 13.5 years ago Sean Davis 21k

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Hello Sean, the the Agi4x44Preprocess package is only for one color Agilent arrays. I also think the limma package is the right choice as it should do the job for two color Agilent arrays. Best regards, Yong Sean Davis wrote: > On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas > <srikanth at="" ibioinformatics.org=""> wrote: >> Hi Everyone, >> >> I would like to know if we have specific package to work with Agilent 4X44k >> array just like Affy. Please guide me how one go for generating HeatMaps and >> other analysis on this data. I am a newbie in this area. > > Take a look at the Agi4x44Preprocess package. If you are new to > microarray data analysis using bioconductor, take a look at the limma > package and its documentation, particularly the user guide. > > Sean > > _______________________________________________ > 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 >

ADD REPLY • link 13.5 years ago Yong Li ▴ 190

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Thanks for quick reply On Tue, Jun 21, 2011 at 6:55 PM, Yong Li <yong.li@zbsa.uni- freiburg.de="">wrote: > Hello Sean, > > the the Agi4x44Preprocess package is only for one color Agilent arrays. I > also think the limma package is the right choice as it should do the job for > two color Agilent arrays. > > Best regards, > Yong > > Sean Davis wrote: > >> On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas >> <srikanth@ibioinformatics.org> wrote: >> >>> Hi Everyone, >>> >>> I would like to know if we have specific package to work with Agilent >>> 4X44k >>> array just like Affy. Please guide me how one go for generating HeatMaps >>> and >>> other analysis on this data. I am a newbie in this area. >>> >> >> Take a look at the Agi4x44Preprocess package. If you are new to >> microarray data analysis using bioconductor, take a look at the limma >> package and its documentation, particularly the user guide. >> >> Sean >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- Srikanth Manda Srinivas Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+917259692031 [[alternative HTML version deleted]]

ADD REPLY • link 13.5 years ago Srikanth Manda Srinivas ▴ 200

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Hi all, I have gone through limma package and now able to work with Agilent 4x44k two color experiment. I have 22 arrays with normal and tumor tissue. I want to draw heatmap for only a set of 10 genes (from all) up-regulated. Please let me know how does one go about choosing a specific set from all RGLists loaded. Thanks in advance Regards, On Tue, Jun 21, 2011 at 8:59 PM, Srikanth Manda Srinivas < srikanth@ibioinformatics.org> wrote: > Thanks for quick reply > > > On Tue, Jun 21, 2011 at 6:55 PM, Yong Li <yong.li@zbsa.uni- freiburg.de="">wrote: > >> Hello Sean, >> >> the the Agi4x44Preprocess package is only for one color Agilent arrays. I >> also think the limma package is the right choice as it should do the job for >> two color Agilent arrays. >> >> Best regards, >> Yong >> >> Sean Davis wrote: >> >>> On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas >>> <srikanth@ibioinformatics.org> wrote: >>> >>>> Hi Everyone, >>>> >>>> I would like to know if we have specific package to work with Agilent >>>> 4X44k >>>> array just like Affy. Please guide me how one go for generating HeatMaps >>>> and >>>> other analysis on this data. I am a newbie in this area. >>>> >>> >>> Take a look at the Agi4x44Preprocess package. If you are new to >>> microarray data analysis using bioconductor, take a look at the limma >>> package and its documentation, particularly the user guide. >>> >>> Sean >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >>> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > > > -- > Srikanth Manda Srinivas > Ph.D. Student > Institute of Bioinformatics > Discoverer, 7th Floor, > International Technology Park, > Bangalore, India > Mob:+917259692031 > > -- Srikanth Manda Srinivas Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+917259692031 [[alternative HTML version deleted]]

ADD REPLY • link 13.5 years ago Srikanth Manda Srinivas ▴ 200

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Hi, Srikanth. If you have an RGList object, you will probably want to do some normalization? Also, you probably want to find differentially-expressed genes? Both of these steps are also detailed in the limma User Guide. Have you done these steps or do you have another method for finding differentially-expressed genes? Sean On Wed, Jun 22, 2011 at 1:35 PM, Srikanth Manda Srinivas <srikanth at="" ibioinformatics.org=""> wrote: > Hi all, > > I have gone through limma package and now able to work with Agilent 4x44k > two color experiment. I have 22 arrays with normal and tumor tissue. I want > to draw heatmap for only a set of 10 genes (from all) up-regulated. Please > let me know how does one go about choosing a specific set from all RGLists > loaded. Thanks in advance > > Regards, > > > > On Tue, Jun 21, 2011 at 8:59 PM, Srikanth Manda Srinivas < > srikanth at ibioinformatics.org> wrote: > >> Thanks for quick reply >> >> >> On Tue, Jun 21, 2011 at 6:55 PM, Yong Li <yong.li at="" zbsa.uni-="" freiburg.de="">wrote: >> >>> Hello Sean, >>> >>> the the Agi4x44Preprocess package is only for one color Agilent arrays. I >>> also think the limma package is the right choice as it should do the job for >>> two color Agilent arrays. >>> >>> Best regards, >>> Yong >>> >>> Sean Davis wrote: >>> >>>> On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas >>>> <srikanth at="" ibioinformatics.org=""> wrote: >>>> >>>>> Hi Everyone, >>>>> >>>>> I would like to know if we have specific package to work with Agilent >>>>> 4X44k >>>>> array just like Affy. Please guide me how one go for generating HeatMaps >>>>> and >>>>> other analysis on this data. I am a newbie in this area. >>>>> >>>> >>>> Take a look at the Agi4x44Preprocess package. ?If you are new to >>>> microarray data analysis using bioconductor, take a look at the limma >>>> package and its documentation, particularly the user guide. >>>> >>>> Sean >>>> >>>> ______________________________**_________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat="" .ethz.ch="" mailman="" listinfo="" bioconductor=""> >>>> Search the archives: http://news.gmane.org/gmane.** >>>> science.biology.informatics.**conductor<http: news.gmane.org="" gma="" ne.science.biology.informatics.conductor=""> >>>> >>>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.science.biology.informatics.conductor=""> >>> >> >> >> >> -- >> Srikanth Manda Srinivas >> Ph.D. Student >> Institute of Bioinformatics >> Discoverer, 7th Floor, >> International Technology Park, >> Bangalore, India >> Mob:+917259692031 >> >> > > > -- > Srikanth Manda Srinivas > Ph.D. Student > Institute of Bioinformatics > Discoverer, 7th Floor, > International Technology Park, > Bangalore, India > Mob:+917259692031 > > ? ? ? ?[[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 >

ADD REPLY • link 13.5 years ago Sean Davis 21k

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Hi Sean, The data is normalized and list of differentially expressed genes is already there with me. I want to draw a heat map for those genes that are upregulated and separate heatmap for downregulated (10 and 6 in each case). Regards, On Wed, Jun 22, 2011 at 11:10 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > Hi, Srikanth. > > If you have an RGList object, you will probably want to do some > normalization? Also, you probably want to find > differentially-expressed genes? Both of these steps are also detailed > in the limma User Guide. Have you done these steps or do you have > another method for finding differentially-expressed genes? > > Sean > > > On Wed, Jun 22, 2011 at 1:35 PM, Srikanth Manda Srinivas > <srikanth@ibioinformatics.org> wrote: > > Hi all, > > > > I have gone through limma package and now able to work with Agilent 4x44k > > two color experiment. I have 22 arrays with normal and tumor tissue. I > want > > to draw heatmap for only a set of 10 genes (from all) up- regulated. > Please > > let me know how does one go about choosing a specific set from all > RGLists > > loaded. Thanks in advance > > > > Regards, > > > > > > > > On Tue, Jun 21, 2011 at 8:59 PM, Srikanth Manda Srinivas < > > srikanth@ibioinformatics.org> wrote: > > > >> Thanks for quick reply > >> > >> > >> On Tue, Jun 21, 2011 at 6:55 PM, Yong Li <yong.li@zbsa.uni- freiburg.de=""> >wrote: > >> > >>> Hello Sean, > >>> > >>> the the Agi4x44Preprocess package is only for one color Agilent arrays. > I > >>> also think the limma package is the right choice as it should do the > job for > >>> two color Agilent arrays. > >>> > >>> Best regards, > >>> Yong > >>> > >>> Sean Davis wrote: > >>> > >>>> On Tue, Jun 21, 2011 at 6:28 AM, Srikanth Manda Srinivas > >>>> <srikanth@ibioinformatics.org> wrote: > >>>> > >>>>> Hi Everyone, > >>>>> > >>>>> I would like to know if we have specific package to work with Agilent > >>>>> 4X44k > >>>>> array just like Affy. Please guide me how one go for generating > HeatMaps > >>>>> and > >>>>> other analysis on this data. I am a newbie in this area. > >>>>> > >>>> > >>>> Take a look at the Agi4x44Preprocess package. If you are new to > >>>> microarray data analysis using bioconductor, take a look at the limma > >>>> package and its documentation, particularly the user guide. > >>>> > >>>> Sean > >>>> > >>>> ______________________________**_________________ > >>>> Bioconductor mailing list > >>>> Bioconductor@r-project.org > >>>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >>>> Search the archives: http://news.gmane.org/gmane.** > >>>> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >>>> > >>>> > >>> ______________________________**_________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.ch/mailman/listinfo/bioconductor> > >>> Search the archives: http://news.gmane.org/gmane.** > >>> science.biology.informatics.**conductor< > http://news.gmane.org/gmane.science.biology.informatics.conductor> > >>> > >> > >> > >> > >> -- > >> Srikanth Manda Srinivas > >> Ph.D. Student > >> Institute of Bioinformatics > >> Discoverer, 7th Floor, > >> International Technology Park, > >> Bangalore, India > >> Mob:+917259692031 > >> > >> > > > > > > -- > > Srikanth Manda Srinivas > > Ph.D. Student > > Institute of Bioinformatics > > Discoverer, 7th Floor, > > International Technology Park, > > Bangalore, India > > Mob:+917259692031 > > > > [[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 > > > -- Srikanth Manda Srinivas Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+917259692031 [[alternative HTML version deleted]]

ADD REPLY • link 13.5 years ago Srikanth Manda Srinivas ▴ 200

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Srinivas Srikanth ▴ 70

@srinivas-srikanth-4708

Last seen 10.3 years ago

Hi Everyone, I would like to know if we have specific package to work with Agilent 4X44k array just like Affy. Please guide me how one go for generating HeatMaps and other analysis on this data. I am a newbie in this area. Regards, -- Srinivas Srikanth Ph.D. Student Institute of Bioinformatics Discoverer, 7th Floor, International Technology Park, Bangalore, India Mob:+917259692031, India Mob:+917259692031 [[alternative HTML version deleted]]

ADD COMMENT • link 13.5 years ago Srinivas Srikanth ▴ 70

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