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Microarray result analysis --
illumina^® platform

The following steps will guide you through the analysis of illumina^® microarray results.
You have to supply your gene list in illumina probeID/target/search_key formats. Other geneID format will be ignored. Up to 20000 target IDs are allowed in a single analyis.

Step one: Choose the microarray platform

Which illumina microarray platform do you use?

Newly released illumina BeadChips®	Previously released illumina BeadChips®
HumanHT-12_V3_0 (Annotated: 2008-11-20) HumanRef-8_V2_0 (Annotated: 2008-11-19) HumanRef-8_V3_0 (Annotated: 2008-11-20) HumanWG-6_V2_0 (Annotated: 2008-11-19) HumanWG-6_V3_0 (Annotated: 2008-11-20) MouseRef-8_V1_1 (Annotated: 2008-12-17) MouseRef-8_V2_0 (Annotated: 2008-11-19) MouseWG-6_V1_1 (Annotated: 2008-12-17) MouseWG-6_V2_0 (Annotated: 2008-11-19) RatRef-12_V1_0 (Annotated: 2008-11-19)	Human-6 v1 Human-6 v2 HumanRef-8 v1 HumanRef-8 v2 Mouse-6 v1 Mouse-6 v1.1 MouseRef-8 v1 MouseRef-8 v1.1 RatRef-12 v1

Step two: Choose the gene ID format you want to use

Illumina uses three kinds of gene identifiers on their microarrays, please choose the identifier you want to use in the following analysis:

For newly released illumina BeadChips®	For previously released illumina BeadChips®
Target (obsolete, not recommented) Search_key (not recommended) Tell me why? ProbeID (recommended)	Target (recommended) Search_key (not recommended) Tell me why? ProbeID (use with caution) Tell me why?

Step three: Upload your gene ID list

Cut and paste your ID list below.

Or alternatively, upload a file containing your IDs.

Text file is required. Each line should have only one ID.

Step Optional: Advanced Parameter Settings

Use default Let me choose

Select statistical test method		Hypergeometric (recommended)		Fisher Exact Test		Χ2 Test
Use Adrian Alexa's improved weighted scoring algorithm?		No (recommended)		Yes (More specific but much slower. Only Fisher Test is available.)
Select multi-test adjustment method		Yekutieli (FDR under dependency) (recommended)	Hochberg (FDR)	Bonferroni	Hochberg	Hommel	Not adjust
Significance Level of Enrichment		0.15 0.1 0.05 0.01 0.001 1e-4 1e-5 We recommed 0.1 for FDR value or 0.01 if not adjust
Minimum # of associated genes in reference (m value) for display		1 2 3 4 5 10 We recommed 5
Graphic result format		PDF (recommended, need Adobe Reader)	PostScript	SVG (might need plug-in)	PNG	GIF	JPEG
Select detail information level		Minimum (Only showing GOID)		Normal (Showing GOID and Term definition)		All (Showing GOID, definition and statistics)
Select font size		6 pt 7 pt 8 pt 9 pt 10 pt 11 pt 12 pt
Optimize the graph width:height ratio		Yes (recommended)	No
Reduce graph size by condensing non-significant nodes to points?		No (recommended)	Yes

Step four: Start analysis

Enter your email address below for sending you the finishing page (required):
   
Name your job below (optional):

Start analysis   Reset
This would take you up to 30 min!
(Note: Up to 15 min extra time is needed if using Adrian Alexa's improved score. See "Advanced Parameter Settings" above for details.)
Your result will be kept for 7 days since your last visit!