Thanks a lot Steve. resolved using is.finite()



On Wed, Jan 29, 2014 at 8:12 PM, Steve Lianoglou
<lianoglou.steve@gene.com>wrote:

> Hi,
>
> On Wed, Jan 29, 2014 at 12:07 AM, Alyaa Mahmoud <alyamahmoud@gmail.com>
> wrote:
> > I also get this error when I simply use plot:
> >
> > plot (df[,1], df[,2])
> > Error in plot.window(...) : infinite axis extents [GEPretty(-inf,inf,5)]
>
> This is not really the right forum for this question, as it is more
> related to base R than Bioc, but anyway:
>
> You must have some weird elements in df[,1] and df[,2] ... and by
> weird, I mean that there are things in there that plot can't plot. Try
> to look at the data and see what's there.
>
> Is the data stored in these columns numeric?
> Are there infinite values?
> Are there NaNs, NAs, etc?
>
> Look at is.finite, is.nan, is.numeric to answer those questions.
> Also looking at `range(df[,1])` (and df[,2]) as well as
> `summary(df[,1])` (and df[,2]) could be helpful.
>
> Trying to plot one axis against a "known good one" could be helpful.
> For instance, assuming these columns are indeed numeric, to test
> df[,1] you could just:
>
> R> plot(df[,1])
>
> and see if you get an error. Try the same for df[,2]
>
> HTH,
>
> -steve
>
> --
> Steve Lianoglou
> Computational Biologist
> Genentech
>



-- 
Alyaa Mahmoud

"Love all, trust a few, do wrong to none"- Shakespeare

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