I would like to measure expression of miRNAs from (Affy) Clariom D arrays. cDNA comes from a PDX mouse model. Since extracting human genetic material from the PDX implicates extracting some mouse cDNA too, I am not sure whether I should remove the human probes that may hybridise with mouse cDNA. I know this approach is reasonable when dealing with transcripts, but I have heard the Affy miRNA arrays contain probes for both human and mouse. Under such scenario, I would not expect mouse genetic material to hybridise with human probes, but with their corresponding mouse probes within the array. Thus, it shouldn't be necessary to exclude the probes from the affy library files, right?