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Probe Set Query by Expression Profile

   Step 1. Select an experiment

        

Please choose Species/Platform/Experiment

   Step 2. Select expression estimation method:

        
             *Notice: 1. RMA estimation values are in log2 scale in filters 1, and original scale is used in other filters;
                       2. To make better informed filter setting,  please first view summary of selected experiment.

   Step 3. Set expression data filtering parameters

General Filter Option:
   Single filter -- Use the first checked filter.
   Multiple filters -- Try all checked filters.
   Composite filters -- Try all checked filters, plus the Boolean combination.

Specific Filter Options:   OR Change to Cross-Experiment Filter  Help
1. Absolute Value Filter: Select probe sets whose absolute values (log2 scaled for RMA) is   and <=  
  A. In >=  arrays from whole experiment   B. In selected arrays from table below.
2.

 MAS5.0 Call Filter:  Select probe sets declared as "Present" by Affymetrix MAS5.0 Suite in
  A. In >=  arrays from whole experiment   B. in selected arrays from table below.
3.

 Variation Filter: Select probe sets whose absolute values change max- min     and ratio max/min >=  fold (For RMA estimation, original scale is used).
  A. In all arrays from whole experiment   B. In selected arrays from table below.
4. Fold Change Filter: Mean of group A must    against group B mean by at least  fold(define groups below).
5. Statistical Test Filter: Please run this filter at Single-Experiment Query
6. ANOVA Filter: Select probe sets with ANOVA p-values   (p-value is for one-way ANOVA under default treatment group membership, as defined in table below. This is useful for simple 1-factor experiments only. For designs with >=2 factors or random effects, please download data to analyze).

7. Composite Filter:   Select several filters, combine them with Boolean Operators "AND"  or "OR". and define precedence with parentheses, i.e. 1 AND ( 2 OR 3).
     


Setup Hybridization Groups
HybridizationTREPFile NameFactor:
genotype		Factor:
time		Two-Sample Test GroupANOVA Group

Notice: (1). Check hybridizations from first column for use in filters 1, 2 or 3, which will use the same hybridizations; (2). set groups in the last 3 columns for filters 4 and 5. N = Not in a group. (3). ANOVA group must be consecutive numbers starting from 1. (4). T= Treatment, REP = Replicate.
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