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Comment: Methylation Analysis experiment design using Limma
by
hortense96
• 0
Hello Sam, Thank you for your feedback ! So I have tried your suggestions by removing myLoad$pd and the cell populations that cause probl…
Comment: Methylation Analysis experiment design using Limma
by
SamGG
▴ 350
I think adding `, myLoad$pd` in model.matrix() is misleading/incorrect. Remove it and try again. Try a simple model such as `~0 +f+NK` in …
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Gordon Smyth
50k
I can't tell you how to analyse your particular dataset. I can only give general advice and help with limma syntax. I don't even know what …
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Chris
• 0
Hi Gordon, Thank you so much for your guide! I don't handle the raw data but a text file with all samples that already normalized as you s…
Comment: Light difference when using coef vs omit a group when compare 3 groups.
by
Gordon Smyth
50k
The MDS plot shows a massive batch effect. If this is a correct plot of your data, then any analysis you have done of this data is worthles…
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DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
Comment: Memory errors using read.bismark?
ashr vs apeglm for interaction data
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