Often it is desirable to exclude some genes from the clustering analysis. For example, MHC and immunogolbulin families genes vary for reasons that are irrelevant to the experiments and analysis of clonal B-cell populations (Bradley Messmer, pers. comm.).
One can make a gene list file (a text file containing probe set names on each line) of collagens genes, by using “Tools/Gene list file by keywords” or from literature search, then in the “Analysis/Filter genes” or “Analysis/Compare samples” dialog specify it as the “Filter on gene list: excluding …” file. The resultant filtering or comparison gene list will not contain these genes.
To remove a list of probe sets completely from the array, specify the gene list as the “Analysis/Open group/other information/probe mask file” to make the CDF.bin file does not contain these gene anymore.
Lastly, if seeing an undesired gene cluster in clustering picture, one can click to highlight this cluster and use “Cluster/Delete selected gene” to exclude these genes so that they do not affect the sample clustering.