[BioC] Time course experiment....

Tue Feb 8 20:30:08 CET 2011

Hi Viritha,

On 02/08/2011 07:01 PM, viritha kaza wrote:
> Hi Marco,
> Thanks for your reply.
> But topTable by default only gives top 10.So how do I know the number in
> topTable fuction which satisfies the criteria of 0.05 that I need to give.
> waiting for your reply...
> Thanks,
> Viritha

the help page of topTable says that you can specify the number of 
returned genes by using the 'number' parameter.
You could set this to the maximum (ie the number of genes you tested) 
and then filter.

HTH.
James.

>
> On Tue, Feb 8, 2011 at 12:35 PM, Manca Marco (PATH)<
> m.manca at maastrichtuniversity.nl>  wrote:
>
>> Hi Viritha,
>>
>> just do
>>
>> code:
>>   design<- model.matrix(~factor(rep(1:2, each=3)))
>>   fit<- lmFit(eset, design)
>>   fit2<- eBayes(fit)
>> top.list<-topTable(fit2,coef=2,adjust="BH")
>> your.results<- top.list[top.list$adj.P.Val<  0.05, ]
>>
>> ...it should do the trick...
>>
>> All the best, Marco
>>
>>
>> --
>> Marco Manca, MD
>> University of Maastricht
>> Faculty of Health, Medicine and Life Sciences (FHML)
>> Cardiovascular Research Institute (CARIM)
>>
>> Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands)
>> Visiting address: Experimental Vascular Pathology group, Dept of Pathology
>> - Room5.08,  Maastricht University Medical Center, P. Debyelaan 25, 6229  HX
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>>
>> E-mail: m.manca at maastrichtuniversity.nl
>> Office telephone: +31(0)433874633
>> Personal mobile: +31(0)626441205
>> Twitter: @markomanka
>>
>>
>>
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>> ________________________________________
>> Da: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org]
>> per conto di viritha [viritha.k at gmail.com]
>> Inviato: martedì 8 febbraio 2011 18.14
>> A: bioconductor at stat.math.ethz.ch
>> Oggetto: Re: [BioC] Time course experiment....
>>
>> Naomi Altman<naomi at ...>  writes:
>>
>>>
>>> I did not get the original posting, but doesn't Sohail just need
>>> "TopTable" for this?
>>>
>>> --Naomi
>>
>> Hi Naomi,
>> I had a similiar issue and used TopTable but I am getting only first 10 but
>> how
>> should I write the code to get selected probesets based on an adjusted
>> p-value
>> less than or equal to 0.05.
>>
>> code:
>>   design<- model.matrix(~factor(rep(1:2, each=3)))
>>   fit<- lmFit(eset, design)
>>   fit2<- eBayes(fit)
>> topTable(fit2,coef=2,adjust="BH")
>>
>> I have 3 control and 3 treated samples.The eset has the probenames and the
>> expression matrix.
>> So my question is how do I get the data of all the probesets which pass
>> this
>> criteria?
>> Thanks,
>> Viritha
>>
>>>
>>> At 08:51 AM 1/2/2006, Gordon Smyth wrote:
>>>> Dear Sohail,
>>>>
>>>> Well, there are lots of ways to generate such a table. Perhaps the
>> simplest
>> is
>>>>
>>>>     fitsel<- fit2[sel.dif, ]
>>>>     as.data.frame( fitsel )
>>>>
>>>> Best wishes
>>>> Gordon
>>>>
>>>>> Date: Tue, 20 Dec 2005 14:03:43 -0500
>>>>> From: "Khan, Sohail"<khan at ...>
>>>>> Subject: [BioC] Time course experiment....
>>>>> To:<bioconductor at ...>
>>>>>
>>>>> Dear List,
>>>>>
>>>>> I have performed a time course analysis using limma, as described in
>>>>> "Bioinformatics and Computational Biology Solutions ........".
>>>>> How can I get a list of differentially expressed genes?  I've tried
>>>>> the code below:
>>>>> sel.dif<-p.adjust(fit2$F.p.vlaue,method="fdr")<0.05
>>>>> This produces a logical vector, right?.  I would like a table of
>>>>> differentially expressed genes with p vales etc.  Sorry, if I missed
>>>>> this in the limma user's guide.  Thanks for any suggestions.
>>>>>
>>>>>
>>>>> Sohail Khan
>>>>> Scientific Programmer
>>>>> COLD SPRING HARBOR LABORATORY
>>>>> Genome Research Center
>>>>> 500 Sunnyside Boulevard
>>>>> Woodbury, NY 11797
>>>>> (516)422-4076
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at ...
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>
>>> Naomi S. Altman                                814-865-3791 (voice)
>>> Associate Professor
>>> Dept. of Statistics                              814-863-7114 (fax)
>>> Penn State University                         814-865-1348 (Statistics)
>>> University Park, PA 16802-2111
>>>
>>
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