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  • Normalizing expression with edgeR - noob needs help

    Hey,

    I'm totally new to the field, I've never used R before but I need to normalize some expression data.

    I have many samples (different source cells) in each file (columns) and many files corresponding to different experiments, which have different numbers of rows (each row is a different gene).

    I want to use RLE normalization which is implemented in the function calcNormFactors from the package edgeR, but I don't understand how can I put the read counts into a matrix since my files contain different numbers of genes (rows).

    I thought I should have a giant matrix containing data from all of my files where the columns are the samples and rows are the genes.

    Should I perhaps take the file that has the highest number of genes and input "0" for these genes if they are not present in the other files?

    Thanks for your time.

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