[BioC] limma ebayes

[James MacDonald]

Hmmm, that would be the old 'didn't quite read the question closely
enough but answered anyway'... 

Thanks for the correction Gordon.

Best,

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
>>> Gordon Smyth <smyth at wehi.edu.au> 01/16/04 8:17 PM >>>
Sorry, Jim, this isn't the problem here. Kninh has used lm.series, not
lmFit.

Gordon

At 12:00 PM 17/01/2004, James MacDonald wrote:
>Actually it is because the release version has a bug when you pass an
>exprSet to lmFit. The devel version has the fix, or you can hack the
>line (about line 30 or so)
>
>if(is.list(object)){
>
>to read
>
>if(is.list(object) & !is(object, "exprSet"){
>
>Best,
>
>Jim
>
>
>
>James W. MacDonald
>Affymetrix and cDNA Microarray Core
>University of Michigan Cancer Center
>1500 E. Medical Center Drive
>7410 CCGC
>Ann Arbor MI 48109
>734-647-5623
> >>> Naomi Altman <naomi at stat.psu.edu> 01/16/04 3:06 PM >>>
>Dear Ken,
>This error message is due to having too many parameters for the number
>of
>observations.  You need to provide:
>
>the experiment design (i.e. how many arrays for each condition and the
>set
>of conditions)
>the design matrix you sent to the program
>
>Without this information, no-one can assist you.
>
>--Naomi Altman
>
>
>At 10:11 AM 1/16/2004, kninh at mdanderson.org wrote:
>
>
> >Hello Limma Developers,
> >I got this error when calling ebayes after  lm.series:
> >
> >Error in ebayes(fit) : No residual degrees of freedom in linear model
>fits
> >
> >I tried both limma 1.3.1 and 1.3.12.   I appreciate your help.
> >
> >thanks,
> >Ken Ninh

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