I have a simple design, but can't seem to find anything on Bioconductor support that addresses the error I am getting. Any help would be much appreciated.
I have a paired design as shown below:
> pData(data.norm) Treatment Patient Age Gender HD 3.1 control 3 25 F HD 3.2 miR92a 3 25 F HD 4.1 control 4 41 F HD 4.2 miR92a 4 41 F HD 19.1 control 19 22 F HD 19.2 miR92a 19 22 F HD 24.1 control 24 35 F HD 24.2 miR92a 24 35 F HD 25.1 control 25 23 F HD 25.2 miR92a 25 23 F
I am trying to find gene expression associated with Treatment while also controlling for age. I used the following design but end up getting NAs for the age coefficient. Is there a better way of modeling this?
# Setup design matrix age <- pData(data.norm)$Age treat <- pData(data.norm)$Treatment sample <- pData(data.norm)$Patient design <- model.matrix(~ sample + treat) # Fit model fit <- lmFit(exprs(data.norm), design)
Coefficients not estimable: age Warning message: Partial NA coefficients for 47323 probe(s)
> sessionInfo() R version 3.2.5 (2016-04-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu precise (12.04.5 LTS) locale:  LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8  LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C  LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:  splines parallel stats graphics grDevices utils datasets methods base other attached packages:  pheatmap_1.0.8 gProfileR_0.5.3 treemap_2.4 gridExtra_2.2.1  knitr_1.12.3 CHBUtils_0.1 dplyr_0.4.3 reshape_0.8.5  arrayQualityMetrics_3.26.1 RColorBrewer_1.1-2 lattice_0.20-33 limma_3.26.8  beadarray_2.20.1 ggplot2_2.1.0 Biobase_2.30.0 BiocGenerics_0.16.1