R Methy IV: Quality Control

Now you will use the QC and normalization steps available in the package minfi.

QC

In order to perform a QC with minfi data, you first need to convert the red and green channels into a methylation signal. You will also create a data.frame containing the sample information. Perform a QC of the raw methylation data, and plot the result. Also do a density plot and a density 'bean' plot.

• Use the function preprocessRaw() to convert the red and green channels into a methylation signal, without using any normalization. Store your preprocessed data in the variable myMinfiPP.
• use the function phenoData <- pData( ) to extract sample information from your raw data.
• rename the columns in phenoData containing information about gender and group to the names gender and Sample_Group.
• Use the function minfiQC() to perform QC on myMinfiPP. Plot the QC using plotQC().
• Use densityPlot() and densityBeanPlot() to illustrate the distribution of beta-values. Remember to use the option sampGroups = phenoData$Sample_Group to color the plots according to the two groups.

Questions

Perform QC analysis and present the following results:

4. A QC plot and an MDS plot
5. A density plot of Beta values

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