r-help volcano plot

[KnifeBoot]

  Can't installe packag maDB or limma.

Error is shown as

Using R version 2.13.1, biocinstall version 2.8.4.
Installing Bioconductor version 2.8 packages:

Is there any other way to draw volcano plot ?

Thanks
        [[alternative HTML version deleted]]

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[Duny]

Use the ggplot2 package in order to make a volcano plot! Check out the following book for more information about the package: ggplot2: Elegant Graphics for Data Analysis (Use R) by Hadley Wickham.  ggplot2 is great for creating professional graphics in no time.    

If you look up stat_density in R, you will find the following example at the bottom of the page:

# Make a volcano plot
ggplot(diamonds, aes(x = price)) +
  stat_density(aes(ymax = ..density..,  ymin = -..density..),
    fill = "grey50", colour = "grey50",
    geom = "ribbon", position = "identity") +
  facet_grid(. ~ cut) +
  coord_flip()

Good luck!
Anna

[Hasan Diwan-2]

On 6 September 2011 08:01, KnifeBoot <[hidden email]> wrote:
>  Can't installe packag maDB or limma.

Which R version, and what platform are you using?
--
Sent from my mobile device
Envoyait de mon telephone mobil

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[bbolker]

Duny <anna.dunietz <at> gmail.com> writes:

>
> Use the ggplot2 package in order to make a volcano plot! Check out the
> following book for more information about the package: ggplot2: Elegant
> Graphics for Data Analysis (Use R) by Hadley Wickham.  ggplot2 is great for
> creating professional graphics in no time.    
>
> If you look up stat_density in R, you will find the following example at the
> bottom of the page:
>
> # Make a volcano plot
> ggplot(diamonds, aes(x = price))

  [snip snip snip]


  ggplot is indeed great, but that looks like a violin plot and
not a volcano plot.  Unless I'm just confused about the terminology
this looks like a typo in the documentation.
  library("sos"); findFn("{volcano plot}") finds a few other
options, but not many.

   To the original poster: can you show us the actual error message?

  Ben Bolker

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[Duny]

Ben - I'm sorry, you're right! The following website shows how to make a volcano plot using ggplot2.
http://bioinformatics.knowledgeblog.org/2011/06/21/volcano-plots-of-microarray-data/

Enjoy!
Anna

[KnifeBoot]

Using R version 2.13.1
Windows 7 Ultimate 64-bit
At 2011-09-06 14:51:09,"Hasan Diwan" <[hidden email]> wrote:
>On 6 September 2011 08:01, KnifeBoot <[hidden email]> wrote:
>>  Can't installe packag maDB or limma.
>
>Which R version, and what platform are you using?
>--
>Sent from my mobile device
>Envoyait de mon telephone mobil

______________________________________________
[hidden email] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.