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Tables 3 and 4 show proportional and cumulative variance expressed by the first 10 PCs, for microarray data extracted from chip U133A and U133B, respectively.
Moreover, we performed GEO computational analysis in microarray data extracted from other publicly available datasets, and compared them with our results.
After hybridization for 17 hours the arrays were washed and scanned using an Agilent scanner and microarray data extracted with Agilent Feature Extraction software.
(3) Beside this, the built-in graphical network visualization tool GraphVis now features the projection of microarray data extracted from EMMA by altering the size of the concerned nodes according to the expression levels of the represented genes (see the application example in additional file 1).
Additional file 9: Description of the 49 genes that exhibited a higher level of expression in somatic embryos (AT-00508) than in callus (AT-00265), torpedo stage zygotic embryos (AT-00629) or leaf tissues (AT-00265), based on microarray data extracted from the Genevestigator tool.
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79 features/attributes were created from mRNA expression microarray profiling data extracted from the Gene Expression Omnibus (GEO) database [ 12] references to the files are provided in the methods and Additional files 1, 2 and 3.
Slides were scanned on the Agilent DNA Microarray Scanner and data extracted using the feature extraction software package (v9.1.3.1) using a standard two-colour protocol.
Slides were scanned on the Agilent DNA Microarray Scanner and data extracted using the feature extraction software package (v9.1.3.1) using a standard two-color protocol.
The microarray was scanned using Agilent Microarray Scanner (G2565CA), and data extracted with Feature Extraction Software v10.7.2.
Microarray data were extracted and analyzed as previously described [27].
To analyze the different formats of microarray data, we extracted microRNA expression data exactly matched to release 10.1.
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