Hi,
We have some unusual PCA patterns from DeSEQ
We have288 individuals from 3 population and two treatments.
When we do a PCA, each population/treatment is separated into two distinct groups (based on 5,000 genes for 288 individuals).
One is treatment “F" with three pop, where each of the three populations is divided into two groups in the first principle component.
The second is treatment “A", where each of the three population is again divided into two groups but this time by the 2nd principle component.
We are most concerned that these divisions within a population/treatment are an artifact of DeSeq normalization.
dlc
We have some unusual PCA patterns from DeSEQ
We have288 individuals from 3 population and two treatments.
When we do a PCA, each population/treatment is separated into two distinct groups (based on 5,000 genes for 288 individuals).
One is treatment “F" with three pop, where each of the three populations is divided into two groups in the first principle component.
The second is treatment “A", where each of the three population is again divided into two groups but this time by the 2nd principle component.
We are most concerned that these divisions within a population/treatment are an artifact of DeSeq normalization.
dlc
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