How to get the normalized counts matrix EDASeq ?
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7.7 years ago
debitboro ▴ 270

Hi Biostars,

how to get the normalized counts matrix after normalizing using the withinLaneNormalization() function of EDASeq package. When I normalize for GC content bias using:

dataWithin <- withinLaneNormalization(data, "gc", which="full")

then I see in the resulted dataframe 3 elements: counts, normalizedCounts, and offset. Is assayData[dataWithin]$normalizedCounts, the normalized counts matrix ?

your response will be appreciated

RNA-Seq normalization within lane normalization • 2.4k views
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