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

[michael watson (IAH-C)]

Well the computational aspect of it is simple.

The limma code states:

df.residual <- fit$df.residual
...
if (all(df.residual == 0)) 
        stop("No residual degrees of freedom in linear model fits")

In your example, fit_NODS7 is the "fit" above.

So it looks like the error is thrown because:

fit_NODS7$df.residual

Is basically a long vector of zeros ie you have no residual degrees of
freedom.

I have to admit I haven't got a clue why this might occur.

Did you get your gene list problems sorted out from a few days ago?

Mick

-----Original Message-----
From: Ankit Pal [mailto:pal_ankit2000 at yahoo.com] 
Sent: 20 May 2005 10:36
To: michael watson (IAH-C)
Cc: bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] LIMMA - No residual degrees of freedom in linear
model fits


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
atall.
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,

-Ankit
--- "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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch 
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> 


		
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