Question: normalization constant in GFOLD
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gravatar for ashish
19 months ago by
ashish200
ashish200 wrote:

I am trying GFOLD on an unreplicated RNA-seq data sets. I have two queries regarding it.

  1. what is the normalization constant and what does the values signify?
  2. In one of the datasets I recieved a warning saying the median of gene read count is zero. What does this mean?
-VL1 Calculating normalization constant ...
-VL1 WARNING: The median of gene read count is zero. The normalization method proposed by DESeq cannot be used. Use total read count to do normalization.
-VL1 Normalization constant is: 
     mouse_15    6.04383e+07    2.61471
     mouse_17    2.31147e+07    1
-VL1 Calculate RPKM ...
  
rna-seq gfold • 463 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by ashish200
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