Difference between revisions of "ModENCODE TilingArray"

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                   Remark Text #Evidence
 
                   Remark Text #Evidence
  
Add tag (under "Result") "Average_expression" for TAR
+
Add tag (under "Result") "Log_expression_level" (of a given TAR of a given Microarray_experiment)
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Developer documentation]]
 
[[Category:Developer documentation]]

Revision as of 00:24, 20 January 2011

This is a documentation about how to handle Affymetrix Tiling Array data, esp. from ModEncode.

Tiling Array Related ACeDB Models

?Microarray - WormBase_Model:Microarray: information about a microarray chip.

Existing object - ?Microarray : Affymetrix_C.elegans_Tiling_Array_1.0R

?Microarray_experiment - WormBase_Model:Microarray_experiment: description of an experiment performed using a microarray.
?Condition - WormBase_Model:Condition: description of an experimental sample used by an microarray experiment.
?Microarray_results - WormBase_Model:Microarray_results: description of direct results for a 'spot' (TAR?) on a microarray from all experiments involving this spot.

Use Microarray_results to store TAR. What should be the Sequence_info for a TAR?

#Microarray_data Result A_vs_B_log_ratio	UNIQUE	Float
                        A_vs_B_SD	UNIQUE	Float
                        Frequency	UNIQUE	Float
                        Number_of_experiments	UNIQUE	Int
                        Range_within_paper	UNIQUE	Float	UNIQUE	Float
                 Confidence	Confidence_level	UNIQUE	Float
                               P_value	UNIQUE	Float
                               Presence      UNIQUE  PA
                                                     PS
                                                     NP
                 Expression_cluster	?Expression_cluster	XREF	Microarray_results
                 Remark	Text	#Evidence

Add tag (under "Result") "Log_expression_level" (of a given TAR of a given Microarray_experiment)