I will use topTable in this case to pick probesets by fold change.

Thank you for the hint Gordon.
-- 
Regards,
Sherosha

2009/1/25 Gordon K Smyth <smyth@wehi.edu.au>

> Dear Sherosha,
>
> If you use
>
>  topTable(fit, coef=c(1,2,3), lfc=1)
>
> then the genes with be ranked by F-statistic, and any probe satisfying lfc
> for any one contrast will be considered.
>
> Regarding decideTests() and method="separate", it doesn't make sense to me
> to use a multiple-contrast cutoff unless you also use a multi-contrast test
> statistic.
>
> Best wishes
> Gordon
>
>
>  Date: Fri, 23 Jan 2009 17:40:07 -0500
>> From: Sherosha Raj <sherosha@gmail.com>
>> Subject: Re: [BioC] Help: LIMMA-decideTests and lfc option
>> To: James MacDonald <jmacdon@med.umich.edu>,
>>        bioconductor@stat.math.ethz.ch
>> Message-ID:
>>        <6cdc8dd00901231440w44b651f4l720d6af746771dfb@mail.gmail.com>
>> Content-Type: text/plain
>>
>> Hi Jim
>> Thank you for the clarification. Is it possible to have a conditional
>> selection based on the lfc in decideTests?
>> Eg. if I had three contrasts and there is a probeset with lfc that
>> satisfies
>> my cutoffs in just ONE contrast but not in the others, and I would still
>> like it to be considered?
>>
>>
>> Thank you again.
>> Regards,
>> Sherosha
>>
>>
>> 2009/1/23 James MacDonald <jmacdon@med.umich.edu>
>>
>>  Hi Sherosha,
>>>
>>> The lfc argument applies to all the contrasts you have made individually.
>>> So for instance if you have three contrasts and for one probeset they
>>> were
>>> (-1.5, 0.3, and 1.1) and you set lfc = 1, then the first and third would
>>> pass that filter and the second would not.
>>>
>>> Best,
>>>
>>> Jim
>>>
>>> James W. MacDonald, M.S.
>>> Biostatistician
>>> Hildebrandt Lab
>>> 8220D MSRB III
>>> 1150 W. Medical Center Drive
>>> Ann Arbor MI 48109-0646
>>> 734-936-8662
>>>
>>>> Sherosha Raj <sherosha@gmail.com> 01/22/09 2:28 PM >>>
>>>>>>
>>>>> Hello everyone
>>>
>>> I am unsure how to interpret the lfc option in the multiple testing
>>> algorithm decideTests:
>>>
>>> decideTests(object,method="separate",adjust.method="BH",p.value=0.05,lfc=0)
>>>
>>> The explanation given is:
>>> "If lfc>0 then contrasts are judged significant only when the
>>> log2-fold change is at least this large in absolute value. For
>>> example, one might choose lfc=log2(1.5) to restrict to 50% changes or
>>> lfc=1 for 2-fold changes. In this case, contrasts must satisfy both
>>> the p-value and the fold-change cutoff to be judged significant."
>>>
>>> What is meant exactly? Is it within a particular contrast that the
>>> log2FC>0 for a particular probeset? Or is it comparing across all the
>>> contrasts specified?
>>>
>>> If some one could offer a clarification  I would be most grateful.
>>> Thank you.
>>>
>>> --
>>> Regards,
>>> Sherosha
>>>
>>

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