Title: Examples of Dynamic Graphics for Microarray Data
1Examples ofDynamic Graphics for Microarray Data
Harold HendersonHarold.Henderson_at_AgResearch.co.n
z
2Dynamic 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!
3Dynamic Graphics Today
- Teaching
- Learning
- CAST, ActivStats
- Statistical practice
- Ggobi Dianne Cook
4Dynamic Graphics
- Simple approach using Data Desk
- Linking, Brush Slice, Identify, Isolate
- Checking
- Spots
- Background
- Slides
- ESTs
- Contigs Continuous Sequences
5Mastitis 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
6Virtual 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
7Background
- Slide 48-80
- Colours Hot to Cold
- By background intensity
- Also colour
- By background Red
- By background Green
Hot/Cold Colour by background intensity
8Foreground
- 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
9Log2red 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
10Slide 48-80
11Yeast Contamination in well
- Bright green background
- Print direction right to left
- in successive rows
- Carryover
- And ESTs from same library in row
12Intensity of spots on slides in print order
These 5 selected green spotsFlagged -100
13Virtual array
- on row and column number
- rather than actual position
14Virtual array
- Top left spot on each the 12 slides
- Spots dont line up across slides on actual X,Y
positions from GenePix
15Trellis
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
16Differentially expressed ESTs
- With Dye reversals
- So see these better after analysis
- For example
- BPMT001726HT
- BPMT001174HT
17(No Transcript)
18(No Transcript)
19Duplicate EST
20Duplicate EST
21219 WATERS
22High WaterH2O 87
- Consistently high on all slides
- Pin row 1 col 3
H2O 87
23High WaterH2O 87
- Consistently high on all slides
- Pin row 1 col 3
- Carryover?
H2O 87
24High WaterH2O 126
- High on slide 84
- High spot and background
25One to the right
26One to the left
27H2O 126 slide 48-84
H2O 126
28Dynamic Graphicsafter Normalisation
- Spatial linear mixed model
- as David discussed
- Among slide analysis
29design 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
30design 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
31EST BPMT001555HT
32Colour pairs and its dye reversal with same cows
33Colours36 hour cow
34Colours and labels 36 hour cow
3519 ESTS with Same contig 010622CS0800042002
36Just 3 of these ESTS with Same Contig
37Other contigs
54 ESTs in one contig
38Some extreme ESTs
36hrcow 695
36hrcow 695
39Data 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
40Visualising 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/