By Robert Gentleman, Vincent Carey, Wolfgang Huber, Rafael Irizarry, Sandrine Dudoit
Complete four-color ebook. a few of the editors created the Bioconductor undertaking and Robert Gentleman is among the originators of R. All tools are illustrated with publicly to be had info, and an incredible component of the e-book is dedicated to totally labored case reports. Code underlying the entire computations which are proven is made to be had on a spouse site, and readers can reproduce each quantity, determine, and desk on their lonesome desktops.
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Additional resources for Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health)
J, we plot Mj = Y2,j − Y1,j versus Aj = (Y2,j + Y1,j )/2. If Y1 and Y2 are logarithmic expression values, then this plot is particularly useful for microarray data, because Mj will represent the log fold change for gene j, and Aj will represent average log intensity for that gene, and both quantities are of interest. pairs and MAplot. pairs function plots all pairwise MA-plots 18 B. M. Bolstad et al. comparing all arrays in the AﬀyBatch. When comparing many arrays, it becomes prohibitive to look at all pairwise comparisons.
Details are available from Wu et al. (2005). To compute the GCRMA expression measure, we need the probe sequences. This information is available, for most mass-produced chip types, from the Bioconductor project via the probe packages. The matchprobes package provides utilities to manipulate the information in the probe packages. When using gcrma, the necessary probe package is determined and loaded automatically. If necessary, the package is automatically downloaded from the Internet and installed.
Here, sensitivity means that a probe’s ﬂuorescence signal indeed responds to changes in the transcript abundance; speciﬁcity, that it does not respond to other transcripts or other types of perturbations. Probes may lack sensitivity. Some probes initially identiﬁed with a gene do not actually hybridize to any of its products. Some probes will have been developed from information that has been superseded. In some cases, the probe may correspond to a diﬀerent gene or it may in fact not represent any gene.
Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health) by Robert Gentleman, Vincent Carey, Wolfgang Huber, Rafael Irizarry, Sandrine Dudoit