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MAGE-TAB introduction: Alvis Brazma (EBI)
1.
MAGE-TAB -
a simple tab delimited format for describing microarray (and potentially other) experiments in a MIAME compliant way MAGE-TAB workshop NCI, January 24, 2008
2.
3.
4.
5. Experiment design
graph Sample 1 Sample 2 Hybridisation Cy3 Cy5 Data
5.
5. Experiment design
graph Sample 1 (Homo S., Brain Sample 2 (Homo S., Kidney) Hybridisation (SMD array 1) Data Protocol (Cy5) Protocol (Cy3) Protocol
6.
liver 1 (Homo
sap.) Hybridisation 1 (HG_U95A) Data1.cel Material processing protocols (P-XMPL-1) Normalisation protocol (P-XMPL-2) liver 2 (Homo sap.) Hybridisation 2 (HG_U95A) Data2.cel Kidney 1 (Homo sap.) Hybridisation 3 (HGU_95A) Data3.cel Brain 1 (Homo sap.) FGDM.txt Kidney 2 (Homo sap.) Brain 2 (Homo sap.)
7.
liver 1 (Homo
sap.) Hybridisation 1 (HG_U95A) Data1.cel Material processing protocols (P-XMPL-1) Normalisation protocol (P-XMPL-2) liver 2 (Homo sap.) Hybridisation 2 (HG_U95A) Data2.cel Kidney 1 (Homo sap.) Hybridisation 3 (HGU_95A) Data3.cel Brain 1 (Homo sap.) FGDM.txt Kidney 2 (Homo sap.) Brain 2 (Homo sap.)
8.
9.
10.
11.
Layers in a
more complex DAG A B C W F E G H I 0 1 2 3 4 5
12.
13.
In reality things
are often even simpler
14.
... or even
simpler than that
15.
v11 v12 v13
(c111, ..., c11n) (c121, ..., c12m) (c113, c ...,) l1 l2 l3 vk1 vk2 vk3 (ck11,..., c11n) (c121, ..., c12m) (c113, ...,) l1 l2 l3 ... ... ...
16.
17.
18.
19.
20.
21.
22.
23.
ADF
24.
25.
26.
27.
liver 1 (Homo
sap.) Hybridisation 1 (HG_U95A) Data1.cel Material processing protocols (P-XMPL-1) Normalisation protocol (P-XMPL-2) liver 2 (Homo sap.) Hybridisation 2 (HG_U95A) Data2.cel Kidney 1 (Homo sap.) Hybridisation 3 (HGU_95A) Data3.cel Brain 1 (Homo sap.) FGDM.txt Kidney 2 (Homo sap.) Brain 2 (Homo sap.)
28.
FGEM.txt: Gene n
… . Gene 3 Gene 2 Gene 1 Hyb 3 (brain) Hyb 2 (kidney) Hyb 1 (liver) Genes
29.
30.
31.
32.
33.
34.
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