User: nilssonp386

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Posts by nilssonp386

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Comment: C: DESeq2: Including known contaminant in the design model does not change PCA plot
... Thank you, sorry I've missed that. Does this take the treatment condition into account when correcting the batch effects, or does the design have to be provided to the ´removeBatchEffect´ function? I've looked in to the limma documentation but they use other input objects to start with. ...
written 12 weeks ago by nilssonp3860
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DESeq2: Including known contaminant in the design model does not change PCA plot
... I have a data set of 51 samples over 4 different conditions, and I want to visualise the similarity between the groups. I have already identified a known blood contamination which affects 7 of the samples, and have added a column named "contamination", with the labels "yes" or "no". However, when I ...
deseq2 written 12 weeks ago by nilssonp3860 • updated 12 weeks ago by Michael Love22k
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Comment: C: edgeR::cpm - Doesn't work on DGEList after update
... Yes, you are totally right. Typing edgeR::cpm solved the problem. ...
written 15 months ago by nilssonp3860
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edgeR::cpm - Doesn't work on DGEList after update
... I have a gene expression data set and want to create a cpm matrix from a DGEList object. Is used to work, but after updating to Bioconductor 3.6, I get the following error message: "unable to find an inherited method for function ‘cpm’ for signature ‘"DGEList". Code provided below. dgList <- DGE ...
edger written 15 months ago by nilssonp3860 • updated 15 months ago by Gordon Smyth37k

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