[BioC] lmFit: Error in dimnames(fit$cov.coefficients)

[Mete Civelek]

Dear Gordon,

Upgrading to the current release of limma solved the problem. I do not get
error messages now. Thank you very much for your help.

Mete

-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
Sent: Monday, November 18, 2013 2:49 PM
To: Mete Civelek
Cc: Bioconductor mailing list
Subject: lmFit: Error in dimnames(fit$cov.coefficients)

Dear Mete,

I have not seen this error before.  The error is occuring after all the
calculations are completed, immediately before lmFit returns its result.

I don't follow your code.  I would expect the subsetting METSIMData[,i] to
cause a problem because you are changing the number of columns of data but
do not appear to be changing the number of rows of the design matrix to
match.  However this sort of mismatch would cause a different error message
to that which is reported.

You might start by upgrading to the current release of Bioconductor (limma
3.18.3).

Also have a close look at the design matrix you are entering to lmFit.

Best wishes
Gordon


> Date: Mon, 18 Nov 2013 02:20:47 -0800
> From: Mete Civelek <mcivelek at mednet.ucla.edu>
> To: <bioconductor at r-project.org>
> Subject: [BioC] lmFit: Error in dimnames(fit$cov.coefficients)
>
> Dear All,
>
> I am getting an error when trying to do an analysis with the lmFit
> function in the limma package. I can't get a handle at what the
> problem might be. I will appreciate any insights you can provide.
> Thank you
>
> Mete
>
> library(limma)
> memory.size(max = TRUE)
> MData<-read.delim("MData.txt", header=T, row.names=1)
> traits<-read.delim("MPheno.txt", header=T) #gene expression in rows,
> samples in columns
> dim(MData)
> #43145 rows, 1396 samples
> #samples in rows
> dim(traits)
> #301 traits and 1396 samples
> ind<-match(names(MData), traits$MOMID) traits<-traits[ind,]
>
> for(j in 136:ncol(traits)){
> form1 <- as.formula(paste(" ~ ",
> paste(names(traits)[c(j,2:19)],collapse="+")))
> design<-model.matrix(form1, data=traits) #Determine the samples with
> NAs in traits i <- !is.na(traits[,j])
> rownames(design)<-colnames(METSIMData[,i])
> fit<-lmFit(METSIMData[,i],design)
> Error in dimnames(fit$cov.coefficients) <- list(coef.names[est],
> coef.names[est]) :
>  attempt to set an attribute on NULL
>
>> sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] parallel  splines   stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] limma_3.16.8         scatterplot3d_0.3-33 WGCNA_1.27-1
> doParallel_1.0.3     iterators_1.0.6      foreach_1.4.1        MASS_7.3-29
>
> [8] reshape_0.8.4        plyr_1.8             cluster_1.14.4
> Hmisc_3.12-2         Formula_1.1-1        survival_2.37-4
> flashClust_1.01-2
> [15] dynamicTreeCut_1.60  impute_1.34.0
>
> loaded via a namespace (and not attached):
> [1] codetools_0.2-8 grid_3.0.1      lattice_0.20-23 rpart_4.1-3
> tools_3.0.1

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