Table 2

Barley expression data sets available for analysis in 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.


Druka et al. BMC Genetics 2008 9:73   doi:10.1186/1471-2156-9-73

Open Data