[BioC] Help on PLGEM R Package Usage

[Norman Pavelka]

Hi Qi,

These fitting values look very outside the optimal range. Do you
actually get a straight line in the ln(sd) vs. ln(mean) plot? If not,
something might be wrong about how the data were normalized. You may
e-mail me offline your data and/or the fitting evaluation plots and I
might be able to diagnose the problem.

The slope is one of the most important parameters to look at, and it
usually should be between 0.5 and 1. The r^2 and Pearson correlation
coefficients should be as close to 1 as possible.

In order to capture the plots in another file format you can call
pdf() prior to run.plgem() to generate a high-quality vector-graphics
PDF file. Example:

library(plgem)
data(LPSeset)
pdf()      # this will open a new PDF file called 'Rplots.pdf'
           # in your current working directory
plgemOutput <- run.plgem(LPSeset)
dev.off()  # this will close the PDF file

Instead of pdf() above you can try bmp(), jpeg(), tiff() or virtually
any other major image file format. Under Windows there is also
win.metafile() that generates EMF image file format.

Hope this helps!
Norman

On Fri, Sep 23, 2011 at 11:06 PM, Wu Qi <qwu at dicp.ac.cn> wrote:
> Dear Norman,
>
>
>
> Thanks for your further advice.
>
> After applying the arguements you recommend, The parameters for my NSAF
> dataset are: slope=0.291, intercept=-5.35, adj.r2=0.636, Pearson=0.464. Are
> they horrible?
>
> Could you tell me which is the most important parameter to assess my dataset
> quality?
>
> And how can I export high quality figure (emf format) with these parameters?
> I could only find it in the simplest wrapper mode. When I append
> “plotFile=TRUE” in run.plgem function, I could only get a png figure whose
> resolution is really poor.
>
>
>
> Best Regards,
>
> Qi Wu