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- Select or enter data for the Fold change fields shown in the following figure and described below.
- Control Sample Set – Select from the drop down list the name of the uploaded control sample set to serve as the fold change reference.
- Regulation Type – Select the term that describes the gene expression in comparison with the control samples: Up is increased expression; Down is decreased expression; Up or Down is increased or decreased; Unchanged means no change in expression.
- Up-Regulation Folds – Enter a numerical value representing fold change. The number you enter here is dependent upon the Regulation Type you selected.
- Up = Up Regulation Folds – Samples with a fold change greater than this value, when compared to the control samples, will be returned.
- Down = Down Regulation Folds – Samples with a fold change less than this value, when compared to the control samples, will be returned.
- Up or Down = Down Regulations Folds, Up Regulation Folds – Samples with a fold change either up or down, when compared to the control samples, will be returned.
- Unchanged = Samples with a fold change between the two specified values will be returned.
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- Genome Interval > Chromosome Number – In the text box that opens, enter the chromosome number you want the query to search against.
- Genome Interval > Chromosome Coordinates – In the From and To text boxes that open, enter the range on the chromosome you want to search. This defines the chromosomal boundaries of the region with the suspected copy number variations.
The Bioconductor DNAcopy algorithm (see on page 68) identifies the location of the amplification or deletion and then reports it as the base pair at the start and stop of the segment. Each segment is then catalogued with chromosome number, start coordinate, stop coordinate, genes in the segment, and the segment mean value.
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