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Bioinformatics with R Cookbook by Paurush Praveen Sinha

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Checking the quality of data

The quality of data can be affected at each step of the microarray experiment pipeline. Quality-related problems could stem from hybridization due to uneven fluorescence on the chip that causes variable intensity distributions. A nonspecific binding or other biological/technical reasons can create background noise in the data. Another possible situation can be an inappropriate experimental design that may affect the dataset as a whole. Using such data will result in wrongful or inconclusive inference during data analysis. Therefore, as analysts we must ensure the data quality before we begin the data analysis. This is achieved by looking for outlying arrays, distributions within arrays, batch effects, and so on. There ...

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