Hi, I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message: Warning message: In lmFit(MA, method = "robust") : Some coefficients not estimable: coefficient interpretation may vary. And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea? Code snipet: #Normalize data with background subtraction MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" ) MA<-normalizeBetweenArrays(MA , method="quantile") #get exp values fit <- lmFit(MA) Thanks, Aaron [[alternative HTML version deleted]]

On Thu, Dec 11, 2008 at 6:02 PM, Skewes,Aaron <askewes at="" mdanderson.org=""> wrote: > Hi, > > I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message: > > Warning message: > In lmFit(MA, method = "robust") : > Some coefficients not estimable: coefficient interpretation may vary. > > And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea? > > Code snipet: > > #Normalize data with background subtraction > MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" ) > MA<-normalizeBetweenArrays(MA , method="quantile") > > #get exp values > fit <- lmFit(MA) Hi, Aaron. You'll need to read the limma user guide and help pages for lmFit and any other functions that you plan to use. To give you a place to start, you will need to define a design matrix before lmFit will be helpful for you. If something in the help and user guide isn't clear, feel free to ask for more detail. Also, when you write to the list, be sure to include the output of sessionInfo(). Hope that helps. Sean

Hi Aaron, Skewes,Aaron wrote: > Hi, > > I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message: > > Warning message: > In lmFit(MA, method = "robust") : > Some coefficients not estimable: coefficient interpretation may vary. > > And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea? All of the coefficients are NA? Not just some of them? The code you show below doesn't jibe with the warning you show above (method = "ls" is the default, so lmFit(MA) should never result in a warning that quotes method = "robust"). I am not sure you have given us enough information. I think at the least we need to see the actual input/output stream from R when you run your code, as well as the number of samples, coefficients you are trying to estimate, and a sessionInfo(). Best, Jim > > Code snipet: > > #Normalize data with background subtraction > MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" ) > MA<-normalizeBetweenArrays(MA , method="quantile") > > #get exp values > fit <- lmFit(MA) > > Thanks, > Aaron > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662

Hi Aaron, Skewes,Aaron wrote: > Hi, > > I am attempting to process a few Agilent 4x44 based arrays using limma. When I try to estimate expression levels with lmFit in limma, I get the following message: > > Warning message: > In lmFit(MA, method = "robust") : > Some coefficients not estimable: coefficient interpretation may vary. > > And all the coeff's are NA. I am not at all sure what the problem is? Can someone give me an idea? All of the coefficients are NA? Not just some of them? The code you show below doesn't jibe with the warning you show above (method = "ls" is the default, so lmFit(MA) should never result in a warning that quotes method = "robust"). I am not sure you have given us enough information. I think at the least we need to see the actual input/output stream from R when you run your code, as well as the number of samples, coefficients you are trying to estimate, and a sessionInfo(). Best, Jim > > Code snipet: > > #Normalize data with background subtraction > MA<-normalizeWithinArrays(RG.Nctr , method="loess", bc.method="rma" ) > MA<-normalizeBetweenArrays(MA , method="quantile") > > #get exp values > fit <- lmFit(MA) > > Thanks, > Aaron > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662