Question: Is CQN compatible with DESeq2?
0
gravatar for nicholas.macknight
22 days ago by
nicholas.macknight0 wrote:

Hi,

I ran conditional quantile normalization on my RNAseq counts. I am then going to use DEseq2. However, DEseq2 only accepts non-negative integers. CQN can be coerced to be non-negative, but is still on the log scale and cannot be coerced into integers. So because DESeq2 only accepts un normalized non-negative integers, then how can the merits of CQN be considered when calculating for differentially expressed genes using DESeq2? Either CQN needs to have an integer normalized output or DESeq2 needs to accept non-integers.

Any help on this is appreciated.

cqn deseq2 • 92 views
ADD COMMENTlink modified 22 days ago by Michael Love26k • written 22 days ago by nicholas.macknight0
Answer: Is CQN compatible with DESeq2?
0
gravatar for Michael Love
22 days ago by
Michael Love26k
United States
Michael Love26k wrote:

We have CQN example code in the vignette. Please take a look there first.

ADD COMMENTlink written 22 days ago by Michael Love26k
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