User: Federico Marini

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Posts by Federico Marini

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Comment: C: Error in pcaplot3d from pcaExplorer, when running Deseq2 since update of package
... As a long term solution, I updated the code to the call for pcaplot3d which was using threejs. The issue was related to some new major changes in rthreejs. It should be fixed now, as in https://github.com/federicomarini/pcaExplorer/commit/95422a244a183329bbd183785e3fef4be5d1ebe4. The changes would ...
written 11 weeks ago by Federico Marini90
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Answer: A: pcaEcplorer PCA2go function crashing
... For the benefit of other users that could encounter the same problem:   It was indeed connected to the fact of being the dataset so small. In the default values of limmaquickpca2go, I use a higher values for the number of genes to use in the PCA and to use for the highest loadings then the actual ...
written 11 weeks ago by Federico Marini90
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Comment: C: pcaEcplorer PCA2go function crashing
... You can use the email address you obtain when typing  maintainer("pcaExplorer") Thank you for trying out in the meanwhile on the airway set. ...
written 12 weeks ago by Federico Marini90
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Answer: A: pcaEcplorer PCA2go function crashing
... I'd probably need the data to tell you more. If you can't do this (e.g. unpublished data or so), would you please to perform the same operations on the data from the airway package? You can do so in a quick way by picking from the code of  library(pcaExplorer) example(pcaExplorer) and then use ...
written 3 months ago by Federico Marini90
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Answer: A: pcaEcplorer PCA2go function crashing
... Hi Reuben, Here's Federico, I am the developer of the package. I'd need a couple of more details to help you find out the cause of the error - first I would try to reproduce it of course. Can you provide me with some details (organism, nr of samples, ...), and send me something like a snippet of ...
written 3 months ago by Federico Marini90
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Answer: A: New function lfcShrink() in DESeq2
... As one of the question-askers, thanks for the clarification! I guess the new shrinkage estimators will be added in the devel branch over time? ...
written 6 months ago by Federico Marini90
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Answer: A: plotPCA - how to add labels to a PCA plot
... I am a big fan of the geom_label_repel, that you can also find directly implemented in the pcaplot function in my package, pcaExplorer (http://bioconductor.org/packages/pcaExplorer/) - note that you would need the ggrepel package ...
written 10 months ago by Federico Marini90
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Answer: A: pcaExplorer error displaying PCA plot
... Hi Janne, it is very likely to be linked to a version of ggrepel VS version of ggplot2. I have the 0.6.4 installed for ggrepel and the issue is gone. See more on a similar issue here: https://github.com/thomasp85/ggraph/issues/10 ...
written 12 months ago by Federico Marini90
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Comment: C: DESeq2 - couple of clarifications
... Thank you for the clarification! As for the LRT vs pairwise, you are right. I wanted at least to prompt the user that (s)he can perform the lrt test when more than 2 levels are available. I also had my personal small portion of pain with using ReportingTools, so I know what you mean - it is still ...
written 12 months ago by Federico Marini90
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DESeq2 - couple of clarifications
... Hey Mike, a couple of questions on DESeq2, but first of all, some code to make my questions reproducible: library(airway) library(DESeq2) library(magrittr) dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),                                               colData = colData(airway),       ...
deseq2 written 12 months ago by Federico Marini90 • updated 12 months ago by Michael Love14k

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