Hello, I am working with 5 affymetrix arrays: 1 wild type and 4 mutants, all differents (no replicates). I think that is the reason why when I run lmFit I get a "subscript out of bound" error. I guess one can't fit a linear model with 1 point only. If it is the case, is there any way around? What would you recommend to analyse these arrays? Thank you very much in advance for your help, Emmanuel ---------- more details ------------------------------------------------------- R: 2.0.1 Package: limma Version: 1.8.16 Date: 2005/01/09 Package: affy Version: 1.5.8-1 Date: 2004-10-20 My phenoData is as follow: > pData(eset2) pheno C1 WT C2 MU1 C3 MU2 C4 MU3 C5 MU5 The design matrix as follow: > design WT MU1 MU2 MU3 MU4 1 1 0 0 0 0 2 0 1 0 0 0 3 0 0 1 0 0 4 0 0 0 1 0 5 0 0 0 0 1 attr(,"assign") [1] 1 1 1 1 1 attr(,"contrasts") attr(,"contrasts")$f [1] "contr.treatment" When I run lmFit, I get an error: > fit = lmFit(eset2, design) Error in inherits(x, "data.frame") : subscript out of bounds

> Date: Tue, 10 May 2005 18:57:51 +0100 > From: Emmanuel Levy <emmanuel.levy@gmail.com> > Subject: [BioC] Limma, lmFit "subscript out of bounds" error > To: bioconductor@stat.math.ethz.ch > > Hello, > > I am working with 5 affymetrix arrays: 1 wild type and 4 mutants, all > differents (no replicates). > I think that is the reason why when I run lmFit I get a "subscript out > of bound" error. > I guess one can't fit a linear model with 1 point only. The code you give shouldn't give an error, and doesn't in limma 1.9.5, but there isn't any point in fitting a linear model to data with no replication. The fitted model will just return your expression matrix back again as coefficients. > If it is the case, is there any way around? What would you recommend > to analyse these arrays? You have 5 different conditions and one array for each condition. The only thing you can do is to compute fold changes (or log-ratios) between the different conditions, and choose an arbitrary cut-off to select genes. This seems intuitively obvious, doesn't it? Gordon > Thank you very much in advance for your help, > > Emmanuel > > ---------- more details ------------------------------------------------------- > R: 2.0.1 > > Package: limma > Version: 1.8.16 > Date: 2005/01/09 > > Package: affy > Version: 1.5.8-1 > Date: 2004-10-20 > > > My phenoData is as follow: >> pData(eset2) > pheno > C1 WT > C2 MU1 > C3 MU2 > C4 MU3 > C5 MU5 > > The design matrix as follow: >> design > WT MU1 MU2 MU3 MU4 > 1 1 0 0 0 0 > 2 0 1 0 0 0 > 3 0 0 1 0 0 > 4 0 0 0 1 0 > 5 0 0 0 0 1 > attr(,"assign") > [1] 1 1 1 1 1 > attr(,"contrasts") > attr(,"contrasts")$f > [1] "contr.treatment" > > When I run lmFit, I get an error: >> fit = lmFit(eset2, design) > Error in inherits(x, "data.frame") : subscript out of bounds