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

[Sean Davis]

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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