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Context\r\n\r\nI noticed that Affymetrix control probes were in the delivered in gene expression matrices that included only samples run on Affymetrix\r\n\r\n```\r\n\tYA_36hpf_rep3 (YA36_5-3)\r\nAFFX-BioB-3\t-0.964241616\r\nAFFX-BioB-5\t-1.101939413\r\nAFFX-BioB-M\t-1.033939384\r\nAFFX-BioC-3\t-0.931904971\r\nAFFX-BioC-5\t-0.949069717\r\nAFFX-BioDn-3\t-0.88990334\r\nAFFX-BioDn-5\t-0.914673485\r\nAFFX-CreX-3\t-1.386955387\r\nAFFX-CreX-5\t-1.242860642\r\nAFFX-DapX-3\t0.923737962\r\nAFFX-DapX-5\t-0.29128977\r\nAFFX-DapX-M\t1.06311269\r\n```\r\n\r\n### Problem or idea\r\n\r\nRemove genes / rows that begin with `AFFX-` which designates that these are the values for the control probes.\r\n\r\n### Solution or next step\r\n\r\nI don't think this is a must have for the initial release and in fact users may not actually mind the inclusion of these probes. I'm filing this ticket in service of keeping track of it and we can see what folks say.\r\n\r\nIf we do end up removing the control probes, it may make sense to include this step in the Affymetrix processor itself. If we decide to implement this after we've processed a lot of Affymetrix data, then I can imagine it makes sense to include this step in the smasher. For that reason, I've tagged this with `smasher` and `processor` labels.\r\n\r\n### New Issue Checklist\r\n\r\n- [x] The title is short and descriptive.\r\n- [x] You have explained the context that led you to write this issue.\r\n- [x] You have reported a problem or idea.\r\n- [x] You have proposed a solution or next step."}}
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