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Instead, it is preferable to generate a type_schema on the fly, based on what is on the array.\r\n\r\nThis still doesn't account for the probesets that do double-duty as main probesets as well as normgene->exon probesets, but I don't know a good way to handle those yet. Here is what I get from a pd.hugene.2.0.st package generated with the updated code:\r\n\r\n> con <- db(pd.hugene.2.0.st)\r\n> dbGetQuery(con, \"select * from type_dict;\")\r\n  type                    type_id\r\n1    1                       main\r\n2    2              control->affx\r\n3    3   control->affx->bac_spike\r\n4    4        control->affx->ercc\r\n5    5 control->affx->polya_spike\r\n6    6  control->bgp->antigenomic\r\n7    7           normgene->intron\r\n8    8                   Reporter\r\n9    9                     rescue\r\n> table(dbGetQuery(con, \"select distinct meta_fsetid, type from featureSet inner join core_mps using(fsetid);\")[,2])\r\n\r\n    1     2     3     4     5     6     7     8     9 \r\n46255    18    18    92    39    23  3575    82  3515 \r\n> load(paste0(path.package(\"pd.hugene.2.0.st\"), \"/extdata/netaffxTranscript.rda\"))\r\n> table(pData(netaffxTranscript)$category)\r\n\r\n             control->affx   control->affx->bac_spike \r\n                        18                         18 \r\n       control->affx->ercc control->affx->polya_spike \r\n                        92                         39 \r\n control->bgp->antigenomic                       main \r\n                        23                      44629 \r\n            normgene->exon           normgene->intron \r\n                      1626                       3575 \r\n                  reporter                     rescue \r\n                        82                       3515 \r\n\r\nNote that the featureSet considers the 1626 normgene->exon probesets to be 'main' probesets. This is because they ARE main probesets when summarized at the 'probeset' level, but when summarized at the 'core' level, they are considered normgene->exon.\r\n\r\n","created_at":"2015-06-04T19:34:21Z","updated_at":"2015-06-04T19:38:33Z","closed_at":"2015-06-04T19:38:33Z","merged_at":"2015-06-04T19:38:33Z","merge_commit_sha":"91ee0cc0453fcc5de1127ac39a575769276ce055","assignee":null,"milestone":null,"commits_url":"https://api.github.com/repos/benilton/pdInfoBuilder/pulls/5/commits","review_comments_url":"https://api.github.com/repos/benilton/pdInfoBuilder/pulls/5/comments","review_comment_url":"https://api.github.com/repos/benilton/pdInfoBuilder/pulls/comments{/number}","comments_url":"https://api.github.com/repos/benilton/pdInfoBuilder/issues/5/comments","statuses_url":"https://api.github.com/repos/benilton/pdInfoBuilder/statuses/54f1d35ea69c0a11648d88dcfd0feaa4b77c59e5","head":{"label":"jmacdon:master","ref":"master","sha":"54f1d35ea69c0a11648d88dcfd0feaa4b77c59e5","user":{"login":"jmacdon","id":5940924,"avatar_url":"https://avatars.githubusercontent.com/u/5940924?v=3","gravatar_id":"","url":"https://api.github.com/users/jmacdon","html_url":"https://github.com/jmacdon","followers_url":"https://api.github.com/users/jmacdon/followers","following_url":"https://api.github.com/users/jmacdon/following{/other_user}","gists_url":"https://api.github.com/users/jmacdon/gists{/gist_id}","starred_url":"https://api.github.com/users/jmacdon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmacdon/subscriptions","organizations_url":"https://api.github.com/users/jmacdon/orgs","repos_url":"https://api.github.com/users/jmacdon/repos","events_url":"https://api.github.com/users/jmacdon/events{/privacy}","received_events_url":"https://api.github.com/users/jmacdon/received_events","type":"User","site_admin":false},"repo":{"id":17095485,"name":"pdInfoBuilder","full_name":"jmacdon/pdInfoBuilder","owner":{"login":"jmacdon","id":5940924,"avatar_url":"https://avatars.githubusercontent.com/u/5940924?v=3","gravatar_id":"","url":"https://api.github.com/users/jmacdon","html_url":"https://github.com/jmacdon","followers_url":"https://api.github.com/users/jmacdon/followers","following_url":"https://api.github.com/users/jmacdon/following{/other_user}","gists_url":"https://api.github.com/users/jmacdon/gists{/gist_id}","starred_url":"https://api.github.com/users/jmacdon/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jmacdon/subscriptions","organizations_url":"https://api.github.com/users/jmacdon/orgs","repos_url":"https://api.github.com/users/jmacdon/repos","events_url":"https://api.github.com/users/jmacdon/events{/privacy}","received_events_url":"https://api.github.com/users/jmacdon/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/jmacdon/pdInfoBuilder","description":"Development 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