Hi I have the following samples: batch [1] 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 2055 1802 1802 2055 [16] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 1802 1802 [31] 1157 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 1802 2055 2055 [46] 2055 2055 2055 2055 2055 2055 2055 2055 2055 2055 Levels: 1157 1802 2055 treatment [1] TCGA-BR-6452 TCGA-BR-6453 tumor TCGA-BR-6454 tumor [6] TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 tumor TCGA-BR-6458 [11] tumor TCGA-BR-6563 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-7196 [16] TCGA-BR-7703 tumor TCGA-BR-7704 tumor TCGA-BR-7707 [21] TCGA-BR-7715 tumor TCGA-BR-7716 tumor TCGA-BR-7717 [26] tumor TCGA-BR-7723 TCGA-CD-5804 TCGA-CG-4437 TCGA-CG-4441 [31] TCGA-CG-4476 TCGA-CG-5716 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 [36] TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 [41] TCGA-D7-6527 TCGA-D7-6528 TCGA-F1-6177 TCGA-F1-6875 TCGA-FP-7735 [46] tumor TCGA-FP-7829 tumor TCGA-HF-7131 TCGA-HF-7132 [51] TCGA-HF-7133 TCGA-HF-7134 TCGA-HF-7136 TCGA-IN-7806 tumor 44 Levels: TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6454 TCGA-BR-6455 ... tumor I want to compare each sample from TCGA_X, to average mutant background, I know it is possible, because I was able to do it using standard commands. However, when I try to adjust for batch effects as follows: design=model.matrix(~batch+treatment) names(data.frame(design)) group=treatment y=readDGE(files, path=wd, columns=c(1,2), group=group) #names(data.frame(design)) design=model.matrix(~0+batch+treatment) names(data.frame(design)) #rownames(design)=colnames(y) design > y = estimateGLMCommonDisp(y, design, verbose=TRUE) Error in glmFit.default(y, design = design, dispersion = dispersion, offset = offset, : Design matrix not of full rank. The following coefficients not estimable: treatmentTCGA-CG-4476 as far as i can tell it is because the batch 1157 contains a normal sample but does not contain any tumor samples. Is there a way around that? Thanks, Eugene -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_3.4.2 limma_3.18.6 loaded via a namespace (and not attached): [1] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.