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Comment: Differing results from plotMDS and PCAtools
by
Fabian
• 0
I really like the visualizations and functionality of the PCAtools package. I looked through this vignette [PCAtools: everything Principa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Gordon Smyth
50k
Regarding your original question, limma results will change if you remove one of the conditions because the residual standard deviations wi…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Chris
• 0
Thank you for reply early on Saturday morning. Sorry if the question is not clear to you. Here is my code when compare 3 conditions: d…
Comment: Differing results from plotMDS and PCAtools
by
Gordon Smyth
50k
The batch effect is not perfectly aligned with sex, with 3 samples not agreeing. I suggest you investigate the two male samples in the top …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
Please make a start on reading the documentation. Perhaps start with Section 1.4 of the [edgeR User's Guide](https://bioconductor.org/packa…
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Answer: Differing results from plotMDS and PCAtools
Comment: Differing results from plotMDS and PCAtools
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Answer: The difference when using Limma compare between 3 conditions vs 2 conditions
A: Removing batch effect with limma::removeBatchEffect() actually exacerbates the e
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