marrayclass5 - Analisis de arreglos Affymetrix Edgar Acuna...

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Unformatted text preview: Analisis de arreglos Affymetrix Edgar Acuna Departamento de Matematicas UPR-Mayaguez Affymetrix GeneChip Hybridized Hybridized Probe Cell Probe Cell 20 m 1.78cm Image of Hybridized Probe Array Image of Hybridized Probe Array Each probe cell contains Each probe cell contains miany copies of a specific miany copies of a specific oligonucleotide probe oligonucleotide probe Single stranded, Single stranded, fluorescently labeled DNA target labeled DNA target Oligonucleotide probe PROBE SET PARA DETECTAR EXPRESION DE GEN (mRNA) X ( 16-20 PROBES) PM = Perfect Match MM = MisMatch Affymetrix GeneChip i = indicador de array (1,., 9) j = indicador de probe pair (1, ., 16-20) PM MM Data and Notation PM ijn , MM ijn = Intensity for perfect/mis-match probe cell j , in chip i , in gene n i = 1,, I (ranging from 1 to hundreds) j=1,, J (usually 16 or 20) n = 1,, N (between 8,000 and 12,000) Los 20 pares PM,MM (datos del nivel del probe) son resumidos en un solo numero para cada gen. Este numero es llamado la medida de expresion del gen y existen varios metodos de determinarlo. Lectura de una image Affymetrix Cerca de 100 pixels por probe cell. Selecciona los16-25 pixels vecinos mas brillantes. Toma el promedio de la intensidad de los pixels seleccionados. La imagen de un chip es capturada en un .CEL file. Los .CEL files contienen las intensidades de todas las probe cells. A diferencia de los arreglos cDNA los arreglos Affymetrix no tienen background como tal. Por lo tanto la correccion por el background de las intensidades de los probe cells es hecha usando las probe cells vecinas. Software for Affymetrix Affymetrix Microarray Suite (MAS 5.1) provided by Affymetrix. Esta descontinuado y ahora se llama Affymetrix Genechip Operating Sofware(GCOS). dChip from www.dchip.org Cheng Li and Wing Wong) Buena presentacion por Baggerly y Combes http://bioinformatics.mdanderson.org/Microarray Course/Lectures05/ma02b.pdf Affy from www.bioconductor.org affy package Pre-procesamiento de arreglos (chips) oligonucleotidos. Plots de diagnosticos, Correcion por el background, Normalizacion del probe-level, Calculo de las medidas de expresion genetica. AffyBatch class cdfName exprs nrow ncol Probe-level intensity data for a batch of arrays (same CDF ) Dimensions of the array Matrices of probe-level intensities and SEs rows probe cells, columns arrays. Name of CDF file for arrays in the batch se.exprs description annotation phenoData Any notes Sample level covariates, instance of class phenoData Name of annotation data MIAME(Minimum information about a Microarray Experiment)information notes Affymetrix chips DAT file: Image file, ~10^7 pixels, ~50 MB. No son usados por Bioconductor CEL file: Cell intensity file, probe level y valores PM y MM....
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marrayclass5 - Analisis de arreglos Affymetrix Edgar Acuna...

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