[BioC] Error in ebayes: No residual degrees of freedom in linear model fits

Wolfgang Huber huber at ebi.ac.uk
Tue May 26 23:38:26 CEST 2009

Lucas Santana dos Santos ha scritto:
> Dear Group,
> I am trying to find differential expressed genes using Limma, however I 
> got the following error when I try eBayes:
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim = 
> stdev.coef.lim) :
> No residual degrees of freedom in linear model fits
> My dataset consists of 8 arrays from 8 different cell lines.  I have no 
> replicates.
> I just want to see which genes are differentially expressed between 
> these cell lines.
> I am wondering if I need more than one array per cell line in order to 
> make this work.
> Maybe eBayes need replicates to generate variability. Does it make sense?
> A similar post already exists: 
> https://stat.ethz.ch/pipermail/bioconductor/2005-May/009027.html
> Thank you,
> Lucas

Dear Lucas

without replication, you will not be able to use limma / eBayes to get 
statistical measures of significance of differential expression.

What you can do is:
- look at the width of distribution of (log-)intensities and eye-ball 
the large-looking ones, or
- decide on a more specific question to ask from your data, or
- ask the people who produced the data to provide replication.

Best wishes

Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber

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