I have a historic microarray dataset from an illumina bead based technology. For my data I only have an dataframe where the columns include, for each sample:
"AVG_Signal" "NARRAYS" "ARRAY_STDEV" "Detection Pval"
I would like to run a comparison analysis using limma to get p adjusted values, however I am not sure what my data corresponds to based on instructions in the limma users guide.
I am more familiar with RNA-seq analysis using DESeq2. However have read posts which suggest Deseq2 is not applicable for microarray - is this correct?
What should I do regarding normalisation and comparison?
The within array normalisation function does not seem applicable.
I have proceeded straight to model.matrix(), lmFit() and makeContrasts() - without any normalisation - however I have only a very small number of differentially expressed genes as a result.
Any advice would be very helpful.
Kind Regards, Alex