NIA Array Analysis Tool

HELP: General description of NIA Array Analysis Tool
Arrayjoin Tool (Windows) for building the input file from multiple scanner files (DOWNLOAD)

Select data file for analysis

Description:

	Array annotation
	Threshold z-value to remove outliers
	Error model
	Size of sliding window for averaging error variances
	Proportion of highest variance values to be removed before variance averaging
	Desirable degrees of freedom for Bayesian error model
	FDR false discovery rate threshold
	Number of permutations
	Number of colors in the array
	Minimum log-intensity cutoff (-9999 = none)
	Maximum log-intensity cutoff (-9999 = none)
	Include reference into ANOVA analysis
	Reference name
	No cross-channel correction

Table of tissues/experiments (see help) N data columns=

# No. of re-
plications Name of tissue/experiment
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Sub-replications
Specify the number of subreplications for each replication through all experiments

Upload Data File:	see file format Normalize Split-normalize
upload as:	Data name (use 1-word; if blank, = filename)
	Log-transformation in input file Lower cutoff value

#	No. of re- plications	Name of tissue/experiment
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135
136
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141
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149
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