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plugins/base1/se.lu.onk.ReplicateError/trunk/lib/pluginConfigurationAA.base

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Rev	Date	Author	Line
22	20 Oct 05	enell	1	BASEfile
22	20 Oct 05	enell	2	section plugin
22	20 Oct 05	enell	3	uniqueName onk.lu.se/enell/ReplicateError
771	18 Sep 08	jari	4	versionNumber @VERSION@
22	20 Oct 05	enell	5	name Filter: ReplicateError (across assays)
2013	01 Aug 13	olle	6	descr Implementation of 'Analysis of replicates' (cf. figure 5 in the publication)\r\nWithin the fold: assessing differential expression measures and reproducibility in microarray assays.\r\nYang IV et al. Genome Biol. 2002 Oct 24;3(11):research0062. Epub 2002 Oct 24.\r\n\r\nParameters:\r\n\r\nStandard deviation limit - Filters out values outside the limit. A limit value <= 0 indicates that no limit is used.\r\n\r\nLeave singletons - Flag indicating if spots occurring once should be leaved.\r\n\r\nassayname - Name of assay.\r\n\r\nGroup\r\n\r\nSort\r\n\r\nCenter of mass - median (default) or mean\r\n\r\nAssays to include
46	22 Nov 05	enell	7	execName runAA
22	20 Oct 05	enell	8	geneAverages 0
22	20 Oct 05	enell	9	serialFormat 0
22	20 Oct 05	enell	10	url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=12429061
22	20 Oct 05	enell	11	minChannels 2
22	20 Oct 05	enell	12	maxChannels 0
33	10 Nov 05	enell	13	leaveStdin 0
33	10 Nov 05	enell	14	leaveStdout 0
22	20 Oct 05	enell	15	estimatedTime 60
22	20 Oct 05	enell	16	defaultMaxRam 67108864
22	20 Oct 05	enell	17	usedColumns position\treporter
22	20 Oct 05	enell	18	usedFields _allIntensities
22	20 Oct 05	enell	19	columns position valueType name commonName options defaultValue enumOptions removed
22	20 Oct 05	enell	20	%
22	20 Oct 05	enell	21	1 h section 30 settings 0
766	16 Sep 08	jari	22	2 e strictReplicate Replicate filter 30 true true\ton\tfalse\toff 1
766	16 Sep 08	jari	23	3 f sdLimit Standard deviation limit 30 2.0 0
766	16 Sep 08	jari	24	4 e newBAS Create new bioassay set 30 true true\tyes\tfalse\tno 1
766	16 Sep 08	jari	25	5 e leaveSingletons Leave singletons 30 false true\tyes\tfalse\tno 0
766	16 Sep 08	jari	26	6 e leaveDataFiles Put gnuplot file in zip archive 30 false true\tyes\tfalse\tno 1
766	16 Sep 08	jari	27	7 t assayname assayname 10 % 0
766	16 Sep 08	jari	28	8 t group Group 10 1 0
766	16 Sep 08	jari	29	9 t sort Sort 10 0
766	16 Sep 08	jari	30	10 e center Center of mass 30 0 0\tmedian\t1\tmean 0
766	16 Sep 08	jari	31	11 t sort Sort 30 1
766	16 Sep 08	jari	32	12 t includeassays Assays to include 30 0