[BioC] LIMMA - No residual degrees of freedom in linear model fits

Ankit Pal pal_ankit2000 at yahoo.com
Fri May 20 11:35:56 CEST 2005

Hi Mick,
Thank you for replying.
I am using 2 arrays. I have a total set of 4 arrays
with 2 dye swaps, I have done an analysis with all the
4 design=c(1,-1,1,-1) and would like to see what the
result is without the dye swaps.
I need to decide if we have to use the dye swaps
I'm looking for genes with a p value < 0.05 after the
moderated t statistic.
I'm not comparing the arrays.
Why so you say 2 arrays is the problem?
How many replicate arrays do you suggest I use to get
reliable results?

>From a previous mail I sent titled "LIMMA- Warning
message after eBayes function",
I got an error for a 2 array alanysis.

> fit_NODS7 <- eBayes(fit_NODS7)

Warning message: 
Estimation of var.prior failed - set to default value
in: ebayes(fit = fit, proportion = proportion,
stdev.coef.lim = stdev.coef.lim)

Is it because of the number of arrays.

Why did the same steps work for other datasets
containing 2 arrays?

Awaiting your reply,

--- "michael watson (IAH-C)"
<michael.watson at bbsrc.ac.uk> wrote:
> Hi Ankit
> What is the design of your experiment?  How many
> arrays do you have and
> what are you trying to find out?  From the
> "design=c(1,1)" bit of your
> code, it looks like you only have two arrays...
> Which may be the
> problem!  Are you trying to compare one array to the
> other?  
> Mick
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On
> Behalf Of Ankit Pal
> Sent: 20 May 2005 09:42
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] LIMMA - No residual degrees of
> freedom in linear model
> fits
> Dear Group,
> On trying to use the eBayes function, I got the
> following error.
> The steps are
> >fit_NODS7 <- lmFit(MA_NODS7, design=c(1,1))
> > fit_NODS7 <- eBayes(fit_NODS7)
> Error in ebayes(fit = fit, proportion = proportion,
> stdev.coef.lim =
> stdev.coef.lim) : 
>         No residual degrees of freedom in linear
> model
> fits
> I understand that the residual degrees of freedom is
> calculated by lmFit().
> So why the error?
> I tried looking up the bioconductor archives, but
> couldn't find any reply that could help solve my
> problem.
> I used the same steps to analyse other datasets
> without any problem.
> I am using the R package version 2.0.1 on a windows
> platform.
> Hoping for a reply,
> Thank you,
> -Ankit
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> Bioconductor at stat.math.ethz.ch
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