Compare samples

Another high-level analysis performed by dChip is the comparison analysis. Given two samples or two groups of samples, we want to identify genes that are reliably differentially expressed between the two groups. dChip provides several filtering criterion to filter out interesting genes. Select menu “Analysis/Compare Samples”:

 

Select one or more arrays in the listbox of the Baseline group and the Experiment group. The current “Array list file” specifies the samples used in the comparison and “pooling replicate arrays” will be performed before the comparison if needed. The pooled replicate arrays are indicated by the ending *’s in the sample name.

If a “Sample information file” is specified in “Analysis/Open Group/Other information” dialog, we can use the “Select by category” button to specify samples with particular annotation:

Check one option among “Overwrite”, “Or”, “And” and “Use inversion” to specify how the specified samples with a particular annotation is combined with the existing selected sample in the “Baseline” and “Experiment” sample list. For example, the “Use inversion” option is for selecting samples not having a particular annotation.