MAGE-TAB introduction: Alvis Brazma (EBI)

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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

What is needed to describe a microarray (and potentially any) experiment adequately (MIAME)? ,[object Object],[object Object],[object Object],[object Object],[object Object]

How to do this? ,[object Object],[object Object],[object Object],[object Object],[object Object]

5. Experiment design graph Sample 1 Sample 2 Hybridisation Cy3 Cy5 Data

5. Experiment design graph Sample 1 (Homo S., Brain Sample 2 (Homo S., Kidney) Hybridisation (SMD array 1) Data Protocol (Cy5) Protocol (Cy3) Protocol

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.)

Important observation ,[object Object],[object Object],[object Object],[object Object],[object Object]

Layers in a more complex DAG A B C W F E G H I 0 1 2 3 4 5

In reality things are often even simpler

v11 v12 v13 (c111, ..., c11n) (c121, ..., c12m) (c113, c ...,) l1 l2 l3 vk1 vk2 vk3 (ck11,..., c11n) (c121, ..., c12m) (c113, ...,) l1 l2 l3 ... ... ...

Ontology usage ,[object Object],[object Object]

Elements to describe an experiment ,[object Object],[object Object],[object Object],[object Object],[object Object]

MAGE-TAB ,[object Object],[object Object],[object Object],[object Object]

Array Design (ADF) ,[object Object],[object Object]

Investigation design file IDF ,[object Object]

Data files ,[object Object],[object Object]

FGEM.txt: Gene n … . Gene 3 Gene 2 Gene 1 Hyb 3 (brain) Hyb 2 (kidney) Hyb 1 (liver) Genes

Experimental Factors ,[object Object],[object Object],[object Object],[object Object]

Standard design templates ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

Some points for later discussion ,[object Object],[object Object],[object Object],[object Object]

Acknowledgements ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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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

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.)

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 ... ... ...

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23. ADF

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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

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