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Limma package can process the chip data, and read more original data formats, including gpr, txt and so on. These file formats are related to the chip image processing software.

After reading the data, we get RGList or EList, the former corresponds to the two-color chip, and the latter corresponds to the monochromatic chip.

In general, the two-color chip RGList needs to go through background correction (backgroundCorrect), intra-chip standardization (normalizeWithinArrays), inter-chip standardization (normalizeBetweenArrays), and finally obtain the standardized MAList.

To view the data distribution of each step, you can draw the MA diagram based on the plotMA provided by limma, or plotDensities to view the density map.

Take GSE121505 data as an example. Get RGList after normal reading, and view the MA diagram and density map of array1:

PlotMA (RGList,array = 1) plotDensities (RGList [, 1])

And the MAList after completing all the corrections

PlotMA (MAList,array = 1) plotDensities (MAList [, 1])

Note: from RGList to the completion of all the correction processes, the object generated in the middle can view the changes in each step according to this method.

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