R package compendium for the analysis of two-color miRNA expression data, during the period of murine embryonic palate development (gestational days (GD) 12, 13, and 14). Samples were hybridized to Miltenyi Biotech miRXplore Microarrays. The compendium covers a wide range of steps which occur in a typical miRNA microarray data analysis, including pre-processing, normalization, differential expression analysis, clustering, target identification, and gene-set enrichment analysis.
Produces plots of clustered expression profiles, with seperate plots for each cluster. The average expression profile for each cluster is superimposed as well.
Filters an RGList object to remove probes with foreground intensities not sufficiently above the background intensity. Additionally can filter probes based on character strings, to remove e.g. control probes.
Imputes missing values in one of the red foreground, red background, green foreground, or green background matrices of an RGList object created from Miltenyi Biotech miRXplore Microarrays. Uses the replicate structure of the array to impute the missing values. Implicit assumption is that only one of the four replicated values for a probe is an missing value.
Imputes outlying values in one of the red foreground, red background, green foreground, or green background matrices of an RGList object created from Miltenyi Biotech miRXplore Microarrays. Uses the replicate structure of the array to impute the outlying values. Implicit assumption is that only one of the four replicated values for a probe is an outlying value.
providing 
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