Difference between revisions of "ModENCODE TilingArray"
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This is a documentation about how to handle Affymetrix Tiling Array data, esp. from ModEncode. | This is a documentation about how to handle Affymetrix Tiling Array data, esp. from ModEncode. | ||
| − | == | + | == Tiling Array Related ACeDB Models == |
| − | |||
| − | [[WormBase_Model:Microarray]]: | + | ?Microarray - [[WormBase_Model:Microarray]]: information about a microarray chip. |
| − | + | Existing object - | |
| − | + | ?Microarray : [http://wormbase.org/db/misc/etree?name=Affymetrix_C.elegans_Tiling_Array_1.0R;class=Microarray;view=expand Affymetrix_C.elegans_Tiling_Array_1.0R] | |
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| − | |||
| − | |||
| − | |||
| + | ?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?) per ?Microarray_experiment. | ||
| + | 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") "Log2_expression" (of a given TAR of a given Microarray_experiment) | ||
| + | |||
| + | ?Expression_cluster - [[WormBase_Model:Expression_cluster]]: to group a set of ?Microarray_results that authors find to have a significant meaning through comparative analysis. | ||
[[Category:Curation]] | [[Category:Curation]] | ||
[[Category:Developer documentation]] | [[Category:Developer documentation]] | ||
Latest revision as of 00:19, 21 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?) per ?Microarray_experiment.
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") "Log2_expression" (of a given TAR of a given Microarray_experiment)
?Expression_cluster - WormBase_Model:Expression_cluster: to group a set of ?Microarray_results that authors find to have a significant meaning through comparative analysis.
