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Normalización de Microarreglos (Genérico)

Bioinformática Posgrado. Normalización de Microarreglos (Genérico). b). Image Analysis and Background Subtraction. Affymetrix. Intensity Value. Image Scanning. Spot Detection. Microarray. Two-dyes. c). Transformation. d). Normalization. M=log2(R/G). Within. Between.

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Normalización de Microarreglos (Genérico)

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  1. Bioinformática Posgrado Normalización de Microarreglos (Genérico)

  2. b) Image Analysis and Background Subtraction Affymetrix IntensityValue Image Scanning Spot Detection Microarray Two-dyes c) Transformation d) Normalization M=log2(R/G) Within Between A=log2(R*G)/2 Microarray Pre-Processing Summary a) Data Processing Image Analysis` Background Detection & Subtraction Background Subtraction Transformation Normalization Summarization Filtering

  3. Columnas en archivo .MEV • UID • IA • IB • R • C • MR  Print-tip Normalization • MC  Print-tip Normalization • SR • SC • FlagA • FlagB • SA • SF • QC • QCA • QCB • BkgA • BkgB • SDA • SDB • SDBkgA • SDBkgB • MedA • MedB • MNA  Signal Ch. A = Cy3 [Green] • MNB Signal Ch. B = Cy5 [Red] • MedBkgA  Background Ch. A • MedBkgB  Background Ch. B • X • Y • PValueA • PValueB

  4. Columnas en GenePix.GPR File • Block  Print-tip Normalization • Column • Row • Name • ID • X • Y • Dia. • F635 Median • F635 Mean • F635 SD • B635 Median • B635 Mean • B635 SD • % > B635 + 1 SD • % > B635 + 2 SD • F635 % Sat. • F532 Median • F532 Mean • F532 SD • B532 Median • B532 Mean • B532 SD • % > B532 + 1 SD • % > B532 + 2 SD • F532 % Sat. • Ratio of Medians • Ratio of Means • Median of Ratios • Mean of Ratios • Ratios SD • Rgn Ratio • Rgn R² • F Pixels • B Pixels • Sum of Medians • Sum of Means • Log Ratio • Flags • Normalize • F1 Median - B1 • F2 Median - B2 • F1 Mean - B1  Signal - Background • F2 Mean - B2  Signal - Background • SNR 1 • F1 Total Intensity • Index • "User Defined" http://www.moleculardevices.com/pages/software/gn_genepix_file_formats.html#gpr

  5. www.gepas.org • CasicualquierMicroarreglo • ExceptoSpotFinder! • MIDAS TM4 NORMALIZACION – Opciones “Fáciles”

  6. Normalizacion usando MIDAS – TM4 (TIGR) • http://www.tm4.org/midas.html • (1) Project  New • (2) Read Data  Single Data File • Especifiquesuarchivo .MEV • (3) Operations LocFit Normalization (Lowess) • “Loc” – Local = por print tip, Lowesso Loess es la normalizaciónde MA

  7. Normalizacion usando MIDAS – TM4 (TIGR) • (4) Write Data • Desactive las casillas “virtual” • (5) Pulse Execution • Esto ejecuta la normalización y escribe algunos archivos. • Escribe 2 carpetas llamadas “raw” (datos crudos u originales) y “lowess” (resultado de la normalización)

  8. Normalizacion usando MIDAS – TM4 (TIGR) • Visualice los resultados en pestaña “Investigation” • De click con el botón derecho en cada rubro y use “Plot” tanto en raw como en lowess

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