Forgot to CC bioclist (sorry): Hi Pravin, On Mon, Oct 1, 2012 at 3:17 AM, PRAVIN <2pravinnilawe at gmail.com> wrote: > Hello, > I am new in using Bioconductor packages for RNA seq experiments. I was > going through the command and modules available for differential gene > expression studies of DESeq. Here i found that there is a module called > plot(). It's not clear what you are referring to. What "different gene expression studies of DESeq" are you talking about? What incantations of `plot` are you referring to? > I couldnt get much information on plot() modules, I wanted to know if this > module can be used to plot graphs like MAplot, etc. to describe DGE studies. I'm curious how you tried to look for such help? I'd read through the DESeq vignette first: http://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc /DESeq.pdf You'll find lots of stuff re: visualizing your data. Also, fire up R, and: R> library(DESeq) R> help(package="DESeq") Will open up a help page -- look for "plot" in there. > Please let me know about it as soon as possible. Hope that was fast enough ... next time, though, please take some time to read through the help that is made available in these packages before asking others to help out. It may seem like it will take you a bit longer in the beginning, but you'll find that your knowledge will beget more knowledge more quickly this way and your terminal velocity will be much higher, if you catch my meaning. 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 -- 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