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Table 2 Barley expression data sets available for analysis in GeneNetwork.

From: Towards systems genetic analyses in barley: Integration of phenotypic, expression and genotype data into GeneNetwork

Types of the expression data sets Data processing description
Barley1 Embryo
gcRMA SCRI
(Dec 06)
Barley1 Leaf
gcRMA SCRI
(Dec 06)
The Affymetrix' CEL files that were generated using MAS 5.0 Suite (Affymetrix, Santa Clara, CA) were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) and processed using the RMA algorithm.
Barley1 Embryo
MAS 5.0 SCRI
(Dec 06)
Barley1 Leaf
MAS 5.0 SCRI
(Dec 06)
The MAS 5.0 values were calculated from the DAT files using Affymetrix' MAS 5.0 Suite (Affymetrix, Santa Clara, CA).
Barley1 Embryo0
gcRMA SCRI
(Apr 06)
Barley1 Leaf
gcRMAn SCRI
(Dec 06)
The Affymetrix' CEL files were imported into the GeneSpring GX 7.3 (Agilent Technologies, Palo Alto, CA) software and processed using the RMA algorithm. Per-chip and per-gene normalization was done following the standard GeneSpring procedure which includes setting the values below 0.01 to 0.01 and then dividing each measurement by the 50th percentile of all measurements in that sample. Additionally each gene was divided by the median of its measurements in all samples.