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Comment: Package needs internet access by firestar ▴ 20

That worked! Thanks! I created the genome file locally and uploaded that. I didn't really think that BSgenome.Hsapiens.UCSC.hg38 was only u…

Comment: limma technical repeat correction by john • 0

Hi @gordonsmyth, Thank you very much for your response. The normalization process involves multiple steps and they provide a normalised f…

Answer: Are unequal sample sizes in differential gene expression (DGE) analysis a proble by Gordon Smyth 51k

No, the imbalance in sample sizes doesn't effect the performance of any of the methods. It is not a problem. You should not be downsampling…

Comment: limma technical repeat correction by Gordon Smyth 51k

I have never analysed SomaScan data, so I cannot make any specific recommendations about how to analyse such data. I have however analysed …

Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela by Gordon Smyth 51k

voom() does not transform the data to be homoscedastic. Quite the opposite, it computes precision weights that reflect the mean-variance tr…

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Answer: Package needs internet access

Dotplot from enricher outputting very few genes

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