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Preparing Affymetrix Data
GENEVA Coordinating Center
Department of Biostatistics
University of Washington
October 15, 20151OverviewThis vignette describes how to prepare Affymetrix data for use in
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01
Step 1: Start by preparing your raw microarray data obtained from Affymetrix.
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Step 2: Normalize the data to remove any technical variations using suitable normalization methods.
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Step 3: Perform quality control checks to ensure the data integrity and identify any potential outliers.
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Step 4: Apply background correction techniques to correct for background noise in the data.
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Step 5: Use probe-level summarization methods to obtain expression values for each gene or probe set.
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Step 6: If required, apply additional filters or data transformation steps to further refine the data.
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Step 7: Perform statistical analysis or other downstream data analyses using the prepared Affymetrix data.
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Step 8: Document the steps followed and the details of data preparation for future reference.
Who needs preparing affymetrix data?
01
Researchers and scientists working in the field of genomics or gene expression analysis.
02
Biostatisticians or bioinformaticians who analyze gene expression data.
03
Pharmaceutical companies or drug discovery laboratories in the process of developing new therapeutics.
04
Academic and research institutions conducting studies on genetic expression patterns.
05
Companies or organizations involved in personalized medicine or diagnostic testing.
06
Any individual or entity working with Affymetrix microarray data for research or commercial purposes.
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