Bioinformatics and Computational Biology Solutions Using R by Robert Gentleman, Vincent Carey, Wolfgang Huber, Rafael

By Robert Gentleman, Vincent Carey, Wolfgang Huber, Rafael Irizarry, Sandrine Dudoit

Complete four-color e-book. many of the editors created the Bioconductor venture and Robert Gentleman is likely one of the originators of R. All equipment are illustrated with publicly on hand facts, and an incredible portion of the booklet is dedicated to completely labored case reports. Code underlying all the computations which are proven is made on hand on a spouse site, and readers can reproduce each quantity, determine, and desk on their lonesome desktops.

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Extra info for Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health)

Example text

We first need to compute the parameters needed for the model. params") Notice this function does not rely on expresso because the PerfectMatch algorithm is not modular. However, the function expressopdnn permits us to perform background correction and normalization steps. 5 Assessing preprocessing methods The existing alternatives for background correction, normalization, and summarization yield a great number of different possible methods for preprocessing probe-level data. Identifying which method is best suited to a given inquiry can be an overwhelming task.

The goal is to use MM when it is physically possible and a quantity smaller than the PM in other cases. This is done by computing the specific background, (SB), for each probeset. This is a robust average of the log ratios of PM to MM for each probe pair in the probeset. 03) and the scaling τ (with a default value of 10), respectively. The adjusted PM intensity is obtained by subtracting the corresponding IM from the observed PM intensity. 2 Normalization As described in Chapter 1 normalization refers to the task of manipulating data to make measurements from different arrays comparable.

In some cases, the probe may correspond to a different gene or it may in fact not represent any gene. , 2001; Knight, 2001). A potential problem especially with short oligonucleotide technology is that the probes may not be specific, that is, in addition to matching the intended transcript, they may also match some other gene(s). In this case, we expect the observed intensity to be a composite from all matching transcripts. Note that here we are limited by the current state of knowledge of the human transcriptome.

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