Pipeline

1
Pipeline
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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 lt- apply( log.intensity, 1, mean,
  trim.1)
• par( mfrowc(3,4), mar c(2,1,2,1))
• plot( density( log.standard))
• for ( ii in 110 ) lines( density(
  log.intensity,ii), colrainbow(10,end.7)ii)
• boxplot( as.data.frame( log.intensity))
• library( geneplotter)
• for ( ii in 110 )
• smoothScatter( log.standard, log.intensity,ii
  - log.standard, ylimc(-1,1) )
• abline( h 0, col2 )
• lines( lowess( log.standard, log.intensity,ii
  - log.standard, f.3 ), col7, lwd2 )

5
(No Transcript)
6
ILM MAQC 1 B D
MDS Plot
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Illumina HapMap
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Ratio-Intensity for ILM HapMap
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Illumina HapMap
MDS Plot
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Agilent MAQC B D
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Agilent MAQC 1 B D
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Agilent MAQC 1 B D
Agilent MDS Plot
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Affymetrix MAQC 1 B D
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Affymetrix MAQC 1 B D
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Affymetrix MAQC 1 B D

• B
• D

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Affymetrix MAQC 1 B D
MDS Plot
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Affymetrix HapMap Subset
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Affymetrix HapMap Subset
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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

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Affymetrix HapMap Subset
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Nimblegen MAQC A B
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Nimblegen MAQC A B
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Nimblegen MAQC A B
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Nimblegen MAQC A B