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Question: RNA-seq edgeR normalization
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gravatar for GuriGuri1565
2.7 years ago by
GuriGuri1565 • 30
GuriGuri1565 • 30 wrote:

I have a matrix. I will enter gene expression values one by one into linear model. if gene1 is input, gene expression values of sample1 ~ sample 10 are input. I wonder how to normalize raw read counts using edgeR and that I can use library size, norm.factors about each genes as a result of calcNormfactors( ).

linear model : y ~ covariate + gene expression value

            gene1        gene2 ... gene24596 
 sample1   read counts
 sample2
   .
   .
   .
 sample10
tmm edger rna-seq normalization • 862 views
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modified 2.7 years ago by Devon Ryan ♦ 98k • written 2.7 years ago by GuriGuri1565 • 30
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gravatar for Devon Ryan
2.7 years ago by
Devon Ryan ♦ 98k
Freiburg, Germany
Devon Ryan ♦ 98k wrote:

Do not reinvent the wheel, your knowledge of statistics is insufficient to do so.

Use edgeR as described in its vignette and DO NOT USE A LINEAR MODEL.
ADD COMMENT • link modified 2.7 years ago • written 2.7 years ago by Devon Ryan ♦ 98k
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