[BioC] help with ACME package

[Sean Davis]

On Tue, Jun 14, 2011 at 9:07 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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.

Hi, Adeolu.

I added a simple write.bedGraph() function to ACME to generate
bedGraph format files for UCSC.  It is available in the devel branch
(in a day or so), version 2.9.1 of ACME.

Sean


>>
>> 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.
>
> Sean
>