On Mon, Jan 17, 2011 at 8:09 AM, David martin <vilanew@gmail.com> wrote:

> Hello,
> I'm having problems computing comparisons between different groups (this is
> not array data and i'm not using limma). Any on what the error must be ?
>
> > mydata.eset
> ExpressionSet (storageMode: lockedEnvironment)
> assayData: 2754598 features, 3 samples
>  element names: exprs
> protocolData: none
> phenoData
>  sampleNames: sampleA sampleB sampleC
>  varLabels: Group Sample
>  varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
>
>
> fit <- lmFit(mydata.eset, design)
> ....
> contrast.matrix
> > contrast.matrix
>                    group1-group2
> group1                                   1
> group2                                      -1
> group3                                       0
>                    group1-group3
> group1                                   1
> group2                                       0
> group3                                      -1
>                    group2-group3
> group1                               0
> group2                                   1
> group3                                  -1
>
> fit2 <- contrasts.fit(fit, contrast.matrix)
> fit2 <- eBayes(fit2)
> Error in ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
>  No residual degrees of freedom in linear model fits
>
>
Hi, David.

You have three samples and three conditions.  That is not enough samples to
perform the tests that you want to perform.  Your only recourse here,
really, is to make ratios among your three arrays and rank genes based on
fold change.  Alternatively, you can go run some biological replicates.

Sean

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