I thank you for your replies Kasper.

The answer on the first one:

nrow(RGset) gives me 622399 features.

On Tue, Sep 4, 2012 at 3:02 PM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> On Tue, Sep 4, 2012 at 4:09 AM, pooja mandaviya
> <pooja.mandaviya@gmail.com> wrote:
> > Hi all,
> >
> > I am kind of new to using R and I have recently started working with
> > Illumina 450K methylation chip and am trying to use the package "minfi"
> for
> > my 780 sample data. While I run my data, I was stuck at small errors and
> > doubts which I wanted to ask and request for your help. I here list them
> > below.
> >
> > 1) densityPlot (RGset, sampGroups = pd$Sample_Group, main = "Beta", xlab
> =
> > "Beta")
> >
> > For this, i get an error saying,
> > Error in density.default(newX[;i],...):
> >      need at least 2 points to select a bandwidth automatically.
> > I get the above error most of the time with most of the datasets i run.
> > Could you help me know how do I get rid with it?
>
> This looks weird, given that I would expect your RGset to have
> 100,000's of rows.  What does
>   nrow(RGset)
> tell you?
>
> > 2)Mset.swan <- preprocessSWAN(RGsetEx, MsetEx)
> >
> > While running this command, it always says,
> >      Normalizing array 1 of 6
> >      Normalizing array 2 of 6
> >      & so on..
> > My question here is that it always shows this and always normalizes the
> > first 6 arrays/samples, but how about the other datasets having more
> than 6
> > samples? I sometimes run a dataset of 100-150 samples. It still shows
> > normalizing 6 samples. How about the rest of the samples?
>
> Well, I hope you use your own data instead of RGsetEx, MsetEx.  The i
> out of n message uses the number of columns (samples) of the input
> data.
>
> > 3) Most of the test datasets run fine, apart from small errors which i
> > listed above. I am also able to get the final plots. However, my main
> > dataset which i have to work on, contains 780 samples. I have tried
> running
> > this through minfi as well. But I always get errors running through most
> of
> > the commands with it. Just to list them here; For commands like QCReport,
> > densityBeanPlot, controlStripPlot, MSet.norm getBetam getM & mdsPlot, I
> get
> > similar errors like
> >
> >> Error: cannot allocate vetor of size 3.6 Gb.
> >> Warning: BISULFITE Conversion 2 probes outside plot range.
> > So my question is that, is minfi not able to support very large datasets?
> > (In my case: 780 samples)
>
> You either need more RAM or you need to run a 64bit R, perhaps both.
>
> > 4) Last question: While normalizing, does minfi also take care of all the
> > batch effects?
>
> No, in general you do not remove batch effects by normalization.
>
> > --
> > Best Wishes,
> >
> > Pooja Mandaviya
> > Department of Clinical Chemistry
> > Erasmus Medical Center, Rotterdam
> > The Netherlands
> > p.mandaviya@erasmusmc.nl
> >
> >
>



-- 
Best Wishes,

Pooja Mandaviya
Department of Clinical Chemistry
Erasmus Medical Center, Rotterdam
The Netherlands
p.mandaviya@erasmusmc.nl

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