Pipeline
Download
1 / 24

Pipeline - PowerPoint PPT Presentation


  • 128 Views
  • Uploaded on

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.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Pipeline' - xandy


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.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Beadchip technology
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
Readin Illumina

  • Read Table – adjust column names

  • Save probe names only once


Preliminary qa ratio intensity
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 )

  • }





Illumina hapmap1
Illumina HapMap

MDS Plot




Agilent maqc 1 b d1
Agilent MAQC 1 B & D

Agilent MDS Plot








Affymetrix hapmap subset2
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







ad