Question: RNA-seq edgeR normalization
0
gravatar for GuriGuri1565
2.7 years ago by
GuriGuri156530
GuriGuri156530 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
ADD COMMENTlink modified 2.7 years ago by Devon Ryan98k • written 2.7 years ago by GuriGuri156530
2
gravatar for Devon Ryan
2.7 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k 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 COMMENTlink modified 2.7 years ago • written 2.7 years ago by Devon Ryan98k
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