Hi,

Highly variable probes are not necessarily differentiating between groups
(if that is what you are aiming at). Please give some more information
about your experiment and what tool / procedure you use for testing and
correction for multiple testing. Also look at

Wilhelm-Benartzi CS, Koestler DC, Karagas MR, Flanagan JM, Christensen BC,
Kelsey KT, et al. Review of processing and analysis methods for DNA
methylation array data. Br J Cancer. 2013;109(6):1394-402.

for some more 450K specific ways to handle this data. I assume you used M
values for filtering, not beta? Please note that the 450K data is in some
fundamental ways different to "regular" gene expression data and that
specific tools might be more applicable. Also see.

Dedeurwaerder S, Defrance M, Bizet M, Calonne E, Bontempi G, Fuks F. A
comprehensive overview of Infinium HumanMethylation450 data processing.
Briefings in bioinformatics. 2013.

Kind regards,
Martin

--
M.A. (Martin) Rijlaarsdam MSc. MD
Erasmus MC - University Medical Center Rotterdam
Department of Pathology
Room Be-432b
Shipping adress: P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
Visiting adress: Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands

Email: m.a.rijlaarsdam@gmail.com
Mobile: +31 6 45408508
Telephone (work): +31 10 7033409
Fax +31 10 7044365
Website: http://www.martinrijlaarsdam.nl


On Tue, May 6, 2014 at 4:43 PM, kaushal [guest] <guest@bioconductor.org>wrote:

>
> Hello list;
>
> I have 450 k human DNA methylation data.  I used genefilter package to get
> the 50% most variable CpG sites that gives me only half of the CpG sites
> for analysis that was originally in 450 K.  However, CpG sites are still
> not significant according to adjsuted p-values.  I am not quite sure what
> could be the reason for this?  Thanks for any insights.
>
> Thanks !!!
>
>
>  -- output of sessionInfo():
>
> None
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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