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Figure 2 | BMC Genomics

Figure 2

From: Specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development

Figure 2

Flow chart of oligo microarray data analysis. Microarray data analysis was performed using GeneSpring 7.2, Agilent Technologies (Palo Alto, CA). Data from a total of 48 slides, containing the intensity values for the control and the signal channels as well as the flag values for present, absent or marginal spots was uploaded and sample attributes were defined. After background subtraction and eliminating all the spots flagged as marginal or absent, data was normalized using an intensity-dependent LOWESS (locally weighted scatter plot smoothing) normalization method to minimize systematic non-biological differences and standardize chips for cross-array comparisons. Normalized data was then filtered on expression level to obtain a group of genes with expression values in at least one of the comparisons made. This group of genes was then used for statistical analysis. A Welch ANOVA (parametric test, variances not assumed equal) was carried out with a p-value cut off 0.05, a false discovery rate (FDR) of 0.05 and between 0.1 and 100 fold expression value change. All members of this collection which contain Gene Ontologies classification for plants information were classified accordingly while the ones without it were manually classified using the GO guidelines. Clustering analysis by k-means grouped genes with similar transcript abundance profiles during germination and emergence in a predefined number of clusters using standard correlation as similarity measure.

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