How do you caculate the normalized value in processed data

iDEP-SDSU / idep

Integrated Differential Expression and Pathway analysis

http://ge-lab.org/idep

121 stars 62 forks source link

How do you caculate the normalized value in processed data #223

Open lizhebio opened 10 months ago

lizhebio commented 10 months ago

The value in the processed data table is neither log2(CPM +4) nor log2(counts + 4). For example, some gene counts value is 2867, the total reads count of this sample is 23860988,
CPM = 2867*10^6/23860988 = 120.152, log2(CPM +4)=6.955; OR log2(2867+ 4) = 11.487 But I got a value of 10.9832 in the processed data table.

Is there some errors?