Sorry for the incomplete message, click the send accidentally.

This analysis is for only one group of 4 biological replicates such as:
                       group
array1              a
array2              a
array3              a
array4              a

I tried to identify the genes which are differently expressed in group a,
but no other reference groups for comparison. Therefore, even all the t
statistics are positive.

Any thoughts? Thanks.



On Tue, Sep 15, 2009 at 11:13 AM, zrl <zrl1974@gmail.com> wrote:

> Hi Heidi,
>
> Thank you for your response. Maybe I didn't make my question very clear.
> This analysis is for only one group of 4 biological replicates such as:
>                        group
> array1
>
>
>
>
> On Tue, Sep 15, 2009 at 4:20 AM, Heidi Dvinge <heidi@ebi.ac.uk> wrote:
>
>>  Hello,
>> you can just sort the topTable result by the t-statistics since these will
>> be either positive or negative, or call it directly with sort.by="t" and
>> then filter for significant p-values.
>>
>> HTH
>> \Heidi
>>
>> On 15 Sep 2009, at 10:05, zrl wrote:
>>
>> Dear List,
>>
>> I have several biological replicates affy arrayes (a simple one group 4
>> arrayes), and tried to use eBayes to get the differentially expressed
>> genes.
>> The topTable ranked the genes by B statistics, which mixed over-expressed
>> genes and under-expressed genes. My question is how I should separate the
>> over and under expressed genes from topTable results. My idea is to
>> calculate the mean average expressed value/intensities (extracted from
>> topTable results with using the number of all the genes) and compare
>> ranked
>> genes with the mean value, if the expressed value is greater than the
>> mean,
>> I take this gene as over-expressed, otherwise, it's under-expressed.
>> Since I don't know the underlying implement of topTable or eBayes, I want
>> to
>> make sure if my method is right. Or you have some better ideas. Thanks.
>>
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>>
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>>
>>
>

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