Examples of Dynamic Graphics for Microarray Data

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Examples ofDynamic Graphics for Microarray Data
Harold HendersonHarold.Henderson_at_AgResearch.co.n
z
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Dynamic Graphics in 1975

• PRIM-9 Dynamic tools for Projecting Rotating Is
  olating Masking 9 or less dimensions
• Developed at ATT Bell LabsFisherkeller,
  Friedman Tukey (1975)
• And a few million dollars of computer equipment!

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Dynamic Graphics Today

• Teaching
• Learning
• CAST, ActivStats
• Statistical practice
• Ggobi Dianne Cook

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Dynamic Graphics

• Simple approach using Data Desk
• Linking, Brush Slice, Identify, Isolate
• Checking
• Spots
• Background
• Slides
• ESTs
• Contigs Continuous Sequences

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Mastitis Experiment

• Kara Swanson, Katarina Domijan
• 6 cows
• Control (C) gland and Infected (I) gland from
  each cow I vs C
• dye reversal of each C vs I
• 6x212 slides
• 22K array
• 270K rows in data

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Virtual Array

• Data from scanned image using GenePix
• 12 slides from same print run (48) with the same
  layout
• The Data Desk files are not included
• Some annotated screen shots from the Data Desk
  presentation follow

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Background

• Slide 48-80
• Colours Hot to Cold
• By background intensity
• Also colour
• By background Red
• By background Green

Hot/Cold Colour by background intensity
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Foreground

• Slide 48-80
• Colours Hot to Cold
• By intensity
• Also colour
• By Red
• By Green
• And by
• A
• M

Hot/Cold Colour by spot intensity
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Log2red on Log2green
Foreground pixels on background pixelsselected
data
All spots
Spotsselected data
Selected data is slide 80 (48-80)
MA plot selected data
Backgroundselected data
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Slide 48-80

• 8x4 32 pins
• Print order

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Yeast Contamination in well

• Bright green background
• Print direction right to left
• in successive rows
• Carryover
• And ESTs from same library in row

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Intensity of spots on slides in print order
These 5 selected green spotsFlagged -100
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Virtual array

• on row and column number
• rather than actual position

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Virtual array

• Top left spot on each the 12 slides
• Spots dont line up across slides on actual X,Y
  positions from GenePix

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Trellis
Dye reversal Dye reversal
Only slight infection
cow 6 cow 5 cow 4 cow 3 cow
2 cow 1
Dye reversal Dye reversal
Dye reversal Dye reversal
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Differentially expressed ESTs

• With Dye reversals
• So see these better after analysis
• For example
• BPMT001726HT
• BPMT001174HT

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Duplicate EST
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Duplicate EST
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219 WATERS
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High WaterH2O 87

• Consistently high on all slides
• Pin row 1 col 3

H2O 87
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High WaterH2O 87

• Consistently high on all slides
• Pin row 1 col 3
• Carryover?

H2O 87
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High WaterH2O 126

• High on slide 84
• High spot and background

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One to the right

• High background

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One to the left

• High background

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H2O 126 slide 48-84
H2O 126
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Dynamic Graphicsafter Normalisation

• Spatial linear mixed model
• as David discussed
• Among slide analysis

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design each with dye reversal

• 36 hour cow
• 53 83 724 459 695 707
• 152 v v
• 690 v v
• 6 hour 691 v v
• cow 742 v v
• 428 v v
• 734 v v

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design as actually run (ie cyclic design broken)

• 36 hour cow
• 53 83 724 459 695 707
• 152 v v
• 690 v v
• 6 hour 691 v v
• cow 742 v v
• 428 v v
• 734 v v

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EST BPMT001555HT
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Colour pairs and its dye reversal with same cows
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Colours36 hour cow
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Colours and labels 36 hour cow
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19 ESTS with Same contig 010622CS0800042002
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Just 3 of these ESTS with Same Contig
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Other contigs
54 ESTs in one contig
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Some extreme ESTs
36hrcow 695
36hrcow 695
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Data Desk

• Download a trial version of from
• www.datadescription.com
• Intro Stats, De Veux Velleman (2004)
• NZ120
• has multimedia ActivStats with Data Desk and DDXL
  excel addin
• lt 231 approx 2x109 cases

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Visualising Data

• www.edwardtufte.com/tufte/
• The visual display of quantitative information
  (1983)
• Envisioning information (1990)
• Visual Explanations (1997)
• The best and the worst of Statistical Graphics
• www.math.yorku.ca/SCS/Gallery/