library(limma)
targets <- readTargets("targets.txt")
RG <- read.maimages(targets$Filename, source = "genepix")
Read GSM3303967_Dcg2699_vs_WT_I.gpr.gz
Read GSM3303968_Dcg2699_vs_WT_II.gpr.gz
Read GSM3303969_Dcg2699_vs_WT_III_csw.gpr.gz
Array 1 corrected
Array 2 corrected
Array 3 corrected
Array 1 corrected
Array 2 corrected
Array 3 corrected
NormExp model for background normalization
Combining probes for a single gene
Clustering
Heathmap
Massive arrays
In situ synthesis
Each oligo has a negative control
Oligos are short. Let’s say 25 bp
There may be several oligos for each gene
Positive match oligos are called \(PM\)
For each \(PM\) there is a negative control called \(MM\)
\(MM\) oligos have a mismatching basepair in the center bp
The \(MM\) probe will not hybridize with the gene, but will hybridize with random fragments
The same random fragments will hybridize with the \(PM\)
The difference \(PM-MM\) is the signal of the gene