1 / 24

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.

xandy
Download Presentation

Pipeline

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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

More Related