I'm trying to combine expression data in R from several experiments performed on different platforms. I have converted all of the probe set names into their corresponding Entrez Gene IDs and then used LIMMA to identify the most powerful probe set for each ID (when there are multiple probe sets mapping to the same gene).
I am planning to construct a single data frame for all of the experiments that contains all of the Entrez Gene IDs examined and all of the samples from the experiments. I thus need a function that will extend existing Entrez IDs' rows and add new rows when I add a new experiment's data set. I had planned to use merge(data, new.data, by=0, all=TRUE) and deal with the NAs later, but I am getting an error telling me "Error in match.names(clabs, names(xi)) : names do not match previous names." A colleague suggested that I cast the data frame as a matrix so that I could merge two matrices, but this doesn't seem to have solved the problem.
Any ideas? Thanks!