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Table 1 Methods available in PreP+07 vs PreP 2003 version

From: PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data

PreP Methods

PreP 03

PreP+ 07

   Background correction

Y

Y

   Logratio conversion

Y

Y

   Block division

Y

Y

   Filtering

N

Y

   Double Scan

Y

Improved

   Lowess per block

Y

Y

   Supervised Lowess

N

Y

   Scaling – Standard Deviation/Median Absolute Deviation – Intraslide/InterSlide

Y

Improved

   Replication

Y

Improved

   Dye Swap

Y

Y

   Stat Test – Local/Global – Ztest Ttest

N

Y

Graphics

  

   Threshold lines

Y

Y

   Slide View

Y

Y

   Coherent Slide View

Y

Y

   Quality Slide View

Y

Y

   MA Graph

Y

Y

   MA Quality Graph

N

Y

   MA per blocks

N

Y

   RG Graph

Y

Y

   Box graph

Y

Y

   Normality graphs (QQ/PN/PP)

N

Y

   Density Graph

Y

Y

   Density Graph per Block

Y

Y

   DoubleScan graphs

Y

Y

   Logratio histogram

Y

Y

   Replication graphs

Y

Y

Others

  

   Zoom

Y

Y

   Online help

N

Y

   Open/Save project

Y

Y

   Save expression Matrix

Y

Improved

   Automatic load of genepix, imagene files

N

Y

   Loading formats automatically

N

Y

   Delete last step

Y

Y

   Delete all steps except last

N

Y

   Toolbar redesigned, related buttons consecutive

N

Y

   Slide Alias when you load it

N

Y

   Apply the same structure with a checkbox button to all loaded slides

N

Y

   Tooltip activation button

N

Y