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]]