Genomic loci with significantly higher DNA methylation in the placenta, relative to maternal blood cells, were identified by the Tiling Array Software (TAS) version 1.1 and the Model-based Analysis of Tiling array (MAT) method with the parameters described in File S1 [28], [28].
All the homozygous mutations were detected, but 8.11% were erroneously reported as heterozygous changes from the reference sequence by the array analysis software.
Student's t-test analysis and log2-transformed signal ratio of each probe set were carried out by the Array Assist Software 5.2.2 (Agilent Technologies, Santa Clara, CA, USA).
Here, W represents the range of possible values for observations, i.e. all positive real-valued intensities generated by the array scanning software (in our case [0, 2 − 1]).
The data obtained were analysed by means of DNASIS array software (Hitachi Software Engineering), which converted the signal intensity for each spot into text format.
The data were analysed by means of DNASIS array software (Hitachi Software Engineering, Tokyo, Japan), which converted the signal intensity for each spot into text format.
The data obtained were analysed by means of DNASIS array software (Hitachi Software Engineering, Yokohama, Japan), which converted the signal intensity for each spot into text format.
Fig. 3 shows the relative expressions of these 75 genes in all the cell lines analyzed by the arrays using the software Pomelo Tool (FDR and p-values for each gene in Additional file 7).
To obtain allelic calls for tumor DNA and the corresponding normal genomic DNA, we used the GDAS® genotyping software supplied by the array manufacturer.
Normalization of raw data was performed by the Array Assist®Software 4.0 (Stratagene, La Jolla, Canada), applying a robust multichip average algorithm with correction for guanine and cytosine content.
