Question: deseq2 rlog trasformation
0
gravatar for jarod_v6@libero.it
2.9 years ago by
Italy
jarod_v6@libero.it40 wrote:

Sorry for this silly question. I use rlog trasfrmation and I found many difference from my samples. There is many values are negative.

 

rld = rlog(dds1)

apply(assay(rld),2,summary)

Min.        0.6044    0.02705   -3.248   -3.063   -2.740   -2.165     -3.181   -3.004
1st Qu.     2.5560    1.75300    4.208    4.335    4.391    3.567      4.165    4.133
Median      3.2620    2.40200    6.626    6.546    6.387    6.328      6.500    6.496
Mean        4.4300    3.53900    6.201    6.149    6.096    5.746      6.180    6.054
3rd Qu.     6.1900    4.46900    8.467    8.297    8.121    8.383      8.443    8.346
Max.       17.5900   17.51000   17.130   16.410   16.680   16.270     17.620   17.500

 

 

Is it normal obtain negative values after trasormation?

 

deseq2 rlog transformation • 390 views
ADD COMMENTlink modified 2.9 years ago by Michael Love25k • written 2.9 years ago by jarod_v6@libero.it40
Answer: deseq2 rlog trasformation
1
gravatar for Michael Love
2.9 years ago by
Michael Love25k
United States
Michael Love25k wrote:

Here's one of the posts I found by searching "rlog negative":

A: Alpha diversity on Rlogtransformed data

ADD COMMENTlink written 2.9 years ago by Michael Love25k
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