Protein Arrays Bioinformatics

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Protein ArraysBioinformatics Statistics
The R package quantmod

• Tim Beissbarth, Achim Tresch

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The long way from Pixels to Protein Intensities
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quantmod Description files
The Slide description file determines for each
block

• which lysate was hybridized
• on which slide
• on which block
• for what purpose
• at which concentration/dilution
• which detection Ab was used
• the detection channel
• the timepoint (optional)

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quantmod Description files
The arraydesign file determines for each spot

• in which block it is located
• its row and column number within the block
• which capture Ab was spotted

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quantmod Slide Intensity files
The Slide intensity files determine for each spot
of a slide

• its position (block,column,row)
• its foreground intensity
• its background intensity
• the flag status

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quantmod Preprocessing
(A list of dilution series)
A dilution series contains the identifier
entries slide, ab1, ab2, substance,
purpose, time and the data series
Plot of one dilution series
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quantmod Preprocessing
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quantmod Preprocessing
Dilution Series Quality Control
Slide description file
Dilution Series Object
Array design file
Slide intensity files
The Antibody combinations file

• lists all Ab1/Ab2 combinations that will be used
  for estimation
• determines how calibrators and measurements will
  be matched
• contains the relative specificities of each
  Ab1/Ab2 combination for the proteins under
  consideration

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Comparison of calibrator lysates
Example of good agreement
Example of bad agreement
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quantmod Preprocessing
Dilution Series Quality Control
Slide description file
Dilution Series Object
Array design file
Slide intensity files
The Abpairs results object is a matrix with

• Identifier entries ab1 ab2 calib.substance
  meas.substance time
• Data entries chat upper lower sd

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quantmod Plotting
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quantmod Plotting
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quantmod User interface
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Outlook
Dilution Series Quality Control
Slide description file
Dilution Series Object
Abpairs Intensity Object
Array design file
Slide intensity files
The Calibration matrix file defines the protein
composition of each calibrator lysate