[BioC] help with ACME package

Sean Davis sdavis2 at mail.nih.gov
Wed Jun 15 03:07:01 CEST 2011

On Tue, Jun 14, 2011 at 6:34 PM, Adeolu Adewoye <badicrown at hotmail.com> wrote:
> Dear Sean,
> I am trying to analyse my NimbleGen MeDIP-chip data using your ACME package
> but have few questions.
> The output file from findRegions command generate suggested enrichment
> regions based on the chosen threshold right? What is the statistical test
> involved ( in order word the output suggested enrichment showing mean and
> median? Is it possible to also output the pValue or probability of
> enrichment?

The  findRegions function simply uses a threshold (default 1e-4)
p-values from a moving-window chi-square test at each probe.  All of
the regions reported by findRegions that have a value of TRUE in the
TF (for True/False) column are considered "positive" and you will need
to play with the findRegions threshold a bit to find what works "best"
for your experiment.  The mean and median values that are output by
findRegions can be used in a ranking fashion with higher means or
medians being "more enriched".

> Can you also please explain a bit more on how to load and view .sgr file in
> the UCSC Genome Browser?

.sgr files are meant to be loaded into the IGB browser.  I do not
think the .sgr file format is supported by the UCSC genome browser.

> Please not that I have tried few things to ask for help using the
> bioconductor distribution list with no response.

Sorry about that.  Thanks for being persistent.


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