I am here trying to perform the differential gene expression analysis between treated samples and untreated samples (vehicle) obtained from the connectivity map (Broad Institute) microarray raw-data. I see the importance of having biological replicates but how would biological replicate apply in the connectivity map raw-data? Because in the connectivity map data they have for example, one treated sample vs one untreated sample. I am only looking at the MCF-7 cell line and HT_HG-U133A array type.
Can someone explain to me what biological replicates are in microarray experiments? Does biological replicate mean one sample i.e. one drug treated microarray sample should be replicated as many as it can be, to increase the reliability? i.e. one drug treated sample x 200 OR as long as the cell lines are the same, if I have 1305 samples with 1305 different drugs with same cell line is a biological replicate?
Wishing to get some insight!