Package limma is one of the best - or even the best - package for reading microarray - and recently RNA-seq - experiment results and doing other process like normalization, fitting linear models, finding top differentially expressed genes, making plots and so on.
I have a minor problem in read.ilmn() function for reading illumina results: Suppose there are some annotation columns - i.e. ENTREZ_GENE_ID, REFSEQ_ID, and so on. These columns are needed to be read in addition to the expression columns - i.e. PROBE_ID, SYMBOL, AVG_Signal and Detection.Pval - for later analysis.
I have tried to pass the names of these columns as the annotation and other.columns arguments of read.ilmn() informing this command to read these columns also, resulting in failure of read.ilmn(). Finally I had to read these columns separately by a read.table() command and merging them manually with read.ilmn() results.
Is there any better way to perform the mission?
I finally solved the problem by manually reading the annotation columns and joining it to the list result of the read.ilmn().