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

[Sean Davis]

On Mon, Feb 6, 2012 at 8:29 AM, Karthik K N <karthikuttan at gmail.com> 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<https://stat.ethz.ch/pipermail/bioconductor/2009-May/027834.html>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.

Hi, Karthik.

The "No residual degrees of freedom" in your case is statistical
language meaning that you do not have enough samples to perform the
number of tests you want to perform.  In your case, this is a problem
because it is not possible to do a statistical hypothesis test with
only two samples.  This is not a software problem but a statistical
issue.  To "fix" the problem, you will need to perform some biologic
replicates.

To deal with your data as-is, you can simply compute a ratio between
treatment and control.

Sean