Hi group,
Thanks for helping me on this.
Viritha

On Wed, Feb 9, 2011 at 5:14 PM, Gordon K Smyth <smyth@wehi.edu.au> wrote:

> Dear Viritha,
>
> To get all genes that pass the FDR<0.05 criterion, you can use
>
>  topTable(fit2, coef=2, n=Inf, p=0.05)
>
> To get all genes that have FDR<0.05 and have log2-fold-change greater than
> 1,
>
>  topTable(fit2, coef=2, n=Inf, p=0.05, lfc=1)
>
> See ?topTable.  Note that 'n' is the upper limit on the number of genes to
> list, not necessarily the actual number to list.
>
> Best wishes
> Gordon
>
>
> Date: Tue, 8 Feb 2011 17:14:42 +0000
>> From: viritha <viritha.k@gmail.com>
>> To: <bioconductor@stat.math.ethz.ch>
>> Subject: Re: [BioC] Time course experiment....
>> Message-ID: <loom.20110208T174927-793@post.gmane.org>
>> Content-Type: text/plain; charset="us-ascii"
>>
>>
>> Naomi Altman <naomi@...> 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
>>
>
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