1. Pipeline

2. BeadChip Technology 50-mer gene- complementary oligo
25-mer identifier oligo
One bead in an etched hole
50,000 beads in each well of 96-well plate

3. Readin Illumina Read Table – adjust column names
Save probe names only once

4. Preliminary QA – Ratio-Intensity
log.standard <- apply( log.intensity, 1, mean, trim=.1)
par( mfrow=c(3,4), mar= c(2,1,2,1))
plot( density( log.standard))
for ( ii in 1:10 ) lines( density( log.intensity[,ii]), col=rainbow(10,end=.7)[ii])
boxplot( as.data.frame( log.intensity))
library( geneplotter)
for ( ii in 1:10 ) {
smoothScatter( log.standard, log.intensity[,ii] - log.standard, ylim=c(-1,1) )
abline( h = 0, col=2 )
lines( lowess( log.standard, log.intensity[,ii] - log.standard, f=.3 ), col=7, lwd=2 ) }

6. ILM MAQC 1 B & D
MDS Plot

7. Illumina HapMap

8. Ratio-Intensity for ILM HapMap

9. Illumina HapMap
MDS Plot

10. Agilent MAQC B & D

11. Agilent MAQC 1 B & D

12. Agilent MAQC 1 B & D
Agilent MDS Plot

13. Affymetrix MAQC 1 – B & D

14. Affymetrix MAQC 1 – B & D

15. Affymetrix MAQC 1 – B & D B D

16. Affymetrix MAQC 1 – B & D
MDS Plot

17. Affymetrix HapMap Subset

18. Affymetrix HapMap Subset

19. Affymetrix HapMap Subset
ID Nbr Corr Row Corr log(PM/MM) avg
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM
GSM

20. Affymetrix HapMap Subset

21. Nimblegen MAQC A & B

22. Nimblegen MAQC A & B

23. Nimblegen MAQC A & B

24. Nimblegen MAQC A & B