Briefly, P-value derived from Wilcoxon rank sum test were calculated for all breast-cancer-study-validated genes in other microarray datasets to check whether significant variation between breast cancer and controls also appeared in those disease datasets.
We have also performed microarray hybridizations to check its usability.
To validate the microarray data and to check for inter-animal variation, RNA's from individual mice were used.
MA plots, boxplots and surface plots for raw and normalized data for each microarray were prepared to check the quality of raw data and the effect of normalization.
To investigate the reliability of the cDNA microarray results and to check if our gene selection was correct, the expression levels of seven genes, PERP, S100A8, FABP5, SFN, CA12, JUP and CSTA, were measured by the qRT-PCR in 22 LN and 49 LN samples.
Immunohistochemistry on tissue microarrays was performed to check NR4A1 protein expression in breast tumours.
One example: Corning is developing a protein array, made in a manner similar to the DNA Microarray, that can be used to check the potential of various substances for use as drugs.
ChIP input DNA was run on an agarose gel to check for microarray optimized DNA fragments of 200 to 1200 bp (Additional file 1: Figure S1A ).
This program allows visual inspection of the entire microarray slide and is used to check the quality of each spot and, if needed, to perform corrections where possible (i.e. for dust or scratches on the surface).
Using Blast2GO a reference set containing all the genes from the custom-made microarray was analyzed and used to check if the GO terms were enriched in a test group (DE genes set) when compared to it by a Fisher's Exact Test with Multiple Testing Correction of FDR [ 59].
