[BioC] help with ACME package

[Fabrice Tourre]

Does anyone try ACME on medip-chip?


On Wed, Jun 15, 2011 at 12:38 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
> 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
>>
>
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