Daniel hi, You can also try the function "lmPerGene" from the new package GSEAlm. This function allows for continuous covariates without recoding them as factors. The function returns an object, say "mylm". To get the t-statistics, divide "mylm$coefficients" by "sqrt(mylm$coef.var)". Note that the coefficients and their variances are matrices with the first row being the intercept. You can then take these t-statistics to your favorite significance/FDR sofware. You can also use it for gene-set-enrichment analysis (see the GSEAlm vignette for more details). If you try to use the function and have more questions, you can write me directly. Assaf