Hi Saroj,

Thanks for your suggestions.

Abhilash



On Thu, Jun 11, 2009 at 8:19 PM, Saroj K Mohapatra <saroj@vt.edu> wrote:

> Hello Abhilash:
>
>> ... where we have 5 normal samples (untreated)
>> with 6 patients treated with drug A and 5 patients treated with drug  A +
>> B.  The biologists question is there any serious perturbations of the
>> genes
>> between two groups (Treated with A only and treated with A+B).
>>
> I agree with your choice: by applying a p.value/ratio threshold in limma
> one can find the genes affected by drug A (A-Control) and genes affected by
> drug A+B (AB-Control). Union of the two sets would have all the genes
> differentially expressed (d.e.) by EITHER treatment; intersection would have
> the genes d.e. in BOTH.
>
>> They are
>> interested to represent the same by a cluster.
>>
>>
> Do you mean a heatmap from hierarchical clustering? You could select the
> genes and then get the expression matrix for all three groups of samples,
> order them by genes only (not samples) and the resulting heatmap would have,
> hopefully, regions of gene expression showing difference between control and
> treatments.
>
> Best,
>
> Saroj
>
>> I am just wondering, whether I should do separate analysis of those two
>> groups using limma and cluster together by selecting genes using some
>> parameters such as P value or fold value.?
>> or
>> Whether I should do analysis together using limma and cluster it by
>> selecting genes by fold value of P value.?
>>
>> It will be of great help if any one of you could provide suggestions on
>> the
>> same.
>>
>> Thanks in advance.
>>
>> Regards,
>> Abhilash
>>
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>>
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>>
>>
>
>


-- 

Regards,
Abhilash

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