[BioC] Important: Help with eBayes in AgiMicrRna and on how to find differentially expressed genes

[Lucas Santana dos Santos]

Karthik,

How does your data looks like? How many arrays do you have?
I jumped in the middle of the thread, and did not get a description of you data.

Lucas 

On Feb 6, 2012, at 9:33 AM, Sean Davis wrote:

> On Mon, Feb 6, 2012 at 9:26 AM, Lucas Santana dos Santos
> <lusasantos at gmail.com> wrote:
>> Hi Karthik,
>> 
>> Since you have two groups, if could use a simple t-test and correct the p-values for multiple testing using Benjamin-hochberg. Besides the t-test, I would suggest to you the sam.r package to find the differentially expressed genes.
>> I have never use BGX with agilent, so I am not sure that this would work.
> 
> Just so Karthik is not mislead, t-tests and other such hypothesis
> tests are not going to be useful without replicates.
> 
> Sean
> 
> 
>> On Feb 6, 2012, at 8:29 AM, Karthik K N wrote:
>> 
>>> Dear Lucas,
>>> 
>>> I am using AgiMicroRna package and came across the same error that you also had i.e., Error in ebayes: No residual degrees of freedom in linear model fits.
>>> 
>>> I read your posts and the replies to that.
>>> 
>>> My dataset consists of just 2 different arrays, one control and one treated. I am trying to find out diferentially expressed genes between them.
>>> 
>>> From the reply to your post I understood the reason why I am seeing this error with eBayes. I just wanted to ask help from you on how will I be able to find out differentially expressed genes between these datasets?
>>> 
>>> I saw you mentioning BGX, but will that work with Agilent miRNA microarray platform? My idea is that it will not.
>>> 
>>> If there is there anything that you can do to help me solve this, I will be really thankful to you.
>>> 
>>> 
>>> Thank you
>>> 
>>> Karthik.
>>> --
>>> Karthik K.N
>>> 
>>> 
>> 
>> 
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>> 
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