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Microarray result analysis --
Affymetrix^® platform

The following steps will guide you through the analysis of Affymetrix^® microarray results.
You have to supply your gene list in Affymetrix probe set ID format. Other geneID format will be ignored. Up to 20000 probe set IDs are allowed in a single analysis.

Step two: Choose the microarray platform

HT Human Genome U133A HT Human Genome U133B Human Genome Focus Array Human Genome HG-U219 Array Human Genome U133 Plus 2.0 Array Human Genome U133 Plus 2.0 Perfect Match Peg Array Human Genome U133A 2.0 Array Human Genome U133A Array Human Genome U133B Array Human Genome U95A Array Human Genome U95Av2 Array Human Genome U95B Array Human Genome U95C Array Human Genome U95D Array Human Genome U95E Array U133_X3P Array

Step three: Select the background type

Select the statistical background you want to use

Whole chip (recommended)
Probesets only for Homo sapiens

Step four: Upload your probe set list

Cut and paste your probe set ID list below.

Or alternatively, upload a file containing your probe set IDs.

Text file is required. Each line should have only one probe set 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 five: 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!