User: jdmontenegroc

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Posts by jdmontenegroc

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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... Thank you Steve, Indeed going through the experimental design I found out the "clones" were not actually clones, but plants from the same "variety" that show fairly similar behaviour and phenotypes, but are not consistent one generation after the next, so yes, there was some variability between the ...
written 5 months ago by jdmontenegroc • 0
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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... Dear Aaron, Thank you for your answer. I agree there are a lot confounding factors I may be missing since I was not part of the original experimental design. I recently found out that the biological repeats that were supposed to be clones, were actually just from the same "variety" and the phenotyp ...
written 5 months ago by jdmontenegroc • 0
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Comment: C: How to determine the cause of no difference between treatments in rnaseq?
... Dear Gordon, Thank you for your answer. I did perform quality checks on the data before doing the DGE test. After filtering genes with fewer than 10 alignments in fewer than 3 libraries I checked the BCV and MDS plots after normalization. The BCVplot shows quite a bit of variation (common dispersio ...
written 5 months ago by jdmontenegroc • 0
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How to determine the cause of no difference between treatments in rnaseq?
... Hello, I recently had a fairly straightforward dge analysis comparing two treatments with three biological replicates each. All samples were clones of the same plant and the tests were performed under the same growth conditions except for the treatment. DGE using the the glmQLFit and glmQLFTest comm ...
rnaseq edger dge written 6 months ago by jdmontenegroc • 0 • updated 6 months ago by Gordon Smyth ♦ 39k

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