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Pipeline

Pipeline. 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. Readin Illumina. Read Table – adjust column names Save probe names only once. Preliminary QA – Ratio-Intensity.

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Pipeline

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  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 ) • }

  5. ILM MAQC 1 B & D MDS Plot

  6. Illumina HapMap

  7. Ratio-Intensity for ILM HapMap

  8. Illumina HapMap MDS Plot

  9. Agilent MAQC B & D

  10. Agilent MAQC 1 B & D

  11. Agilent MAQC 1 B & D Agilent MDS Plot

  12. Affymetrix MAQC 1 – B & D

  13. Affymetrix MAQC 1 – B & D

  14. Affymetrix MAQC 1 – B & D • B • D

  15. Affymetrix MAQC 1 – B & D MDS Plot

  16. Affymetrix HapMap Subset

  17. Affymetrix HapMap Subset

  18. Affymetrix HapMap Subset • ID Nbr Corr Row Corr log(PM/MM) avg • GSM25349 0.1373707 0.9768381 0.4402111 • GSM25350 0.1536714 0.9641 0.4107407 • GSM25356 0.1789144 0.9782233 0.4504628 • GSM25357 0.1822639 0.9608214 0.3933462 • GSM25358 0.164412 0.9780766 0.5120767 • GSM25359 0.2790509 0.9372077 0.5337625 • GSM25360 0.1589303 0.9705504 0.3983221 • GSM25361 0.1074465 0.9693632 0.4023586 • GSM25377 0.2195064 0.9451837 0.3152701 • GSM25378 0.1879018 0.9416335 0.5537572 • GSM25385 0.09208453 0.976753 0.5079342 • GSM25386 0.1340507 0.963868 0.3283866 • GSM25399 0.1958363 0.9333612 0.3169583 • GSM25400 0.110312 0.9903046 0.5331069 • GSM25401 0.1914453 0.9646998 0.4121351 • GSM25402 0.1161411 0.9916095 0.4261114

  19. Affymetrix HapMap Subset

  20. Nimblegen MAQC A & B

  21. Nimblegen MAQC A & B

  22. Nimblegen MAQC A & B

  23. Nimblegen MAQC A & B

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