Genomics Suite Documentation

PGS Documentation

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SubtitleTextSection of the contrasts setup dialog with an example of two contrasts
AnchorNametwo contrasts specified

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Push OK to confirm the contrast (and close the contrast dialog) and again to start the ANOVA calculation.

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SubtitleTextProcessing the annotation file. User needs to point to the columns of the annotation file that contain the probe identifier as well as the chromosome and coordinates of the probe.
AnchorNamespecify genomic position

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The result of 1-way ANOVA is shown in Figure 5. Each row of the table represents a single CpG locus (identified by Probeset ID column). The remaining columns contain the following information:

3. Gene Symbol: the gene overlapping the probe as specified in the Illumina manifest file

4. p-value(HPSC): overall p-value for the specified factor (in parenthesis). A low p-value indicates that there is a difference in methylation between the levels of this attribute (i.e. study groups). The contrast p-values should then be used to evaluate individual group comparisons. If more than one factor is included in the model, p-value will be reported for each.

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SubtitleTextANOVA spreadsheet (truncated). Each row is a result of an ANOVA at a given CpG locus (identified by the Probeset ID columns). The remaining columns contain annotation and statistical output
AnchorNameANOVA Spreadsheet

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