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

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@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Ankit Pal Sent: 20 May 2005 09:42 To: bioconductor@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@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor

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@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@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On > Behalf Of Ankit Pal > Sent: 20 May 2005 09:42 > To: bioconductor@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Discover Yahoo! Use Yahoo! to plan a weekend, have fun online and more. Check it out!

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@yahoo.com] Sent: 20 May 2005 10:36 To: michael watson (IAH-C) Cc: bioconductor@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@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@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On > Behalf Of Ankit Pal > Sent: 20 May 2005 09:42 > To: bioconductor@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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Discover Yahoo! Use Yahoo! to plan a weekend, have fun online and more. Check it out! http://discover.yahoo.com/