[BioC] Bumphunter output

[Kasper Daniel Hansen]

Ok, then your output should include some measure of significance,
which has changed a bit recently.  You need to select regions that
have a low FWER, or however you want to do.  But it is important to
understand that the output is merely candidate regions and (if you do
permutation testing) each region should have some associated measure
of significance.

Kasper

On Mon, Feb 18, 2013 at 10:12 AM, khadeeja ismail <hajjja at yahoo.com> wrote:
> But the bumphunter function does that, right? I set B to 1000.
> Khadeeja
>
>
> ________________________________
> From: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>
> To: khadeeja ismail <hajjja at yahoo.com>
> Cc: "bioconductor at r-project.org" <bioconductor at r-project.org>
> Sent: Monday, February 18, 2013 5:09 PM
> Subject: Re: [BioC] Bumphunter output
>
> You need to do permutation testing, by setting B=some number.
>
> Kasper
>
> On Mon, Feb 18, 2013 at 9:48 AM, khadeeja ismail <hajjja at yahoo.com> wrote:
>> Hi All,
>> I have a question about the output from the bumphunter package. Can I take
>> all the regions in $tab as significant bumps or is there any other cut-off
>> that I need to apply?
>> Thanking you in advance,
>> Khadeeja
>>        [[alternative HTML version deleted]]
>>
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>