User: s.w.vanderlaan

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Posts by s.w.vanderlaan

<prev • 8 results • page 1 of 1 • next >
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Error invalid class "SummarizedExperiment" when using library("MultiDataSet")
... Hi, I have two SummarizedExperiments: one is methylation and the other RNAseq data. I'd like to combine it using the MultiDataSet library to be able to run linear regression models between methylation and RNAseq data. I've combined the two SE's into one, using the code below: multi <- create ...
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Comment: C: Standard error and effect size from Limma
... Ah, thank you for the answer, this was not immediately clear to me.   ...
written 3 months ago by s.w.vanderlaan20
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Comment: C: Standard error and effect size from Limma
... However, I'm following this protocol here: https://molepi.github.io/DNAmArray_workflow/06_EWAS.html#correct_for_bias_and_inflation to run a EWAS. So, we start with limma(), but correct for inflation using bacon(). And thus, this is my code.  designp <- model.matrix(metadata(Mvalues)$formula, da ...
written 3 months ago by s.w.vanderlaan20
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Comment: C: Standard error and effect size from Limma
... I'm sorry, just tried this code, but in my `fit` object I don't have 's2.post'. How do I get this? ...
written 3 months ago by s.w.vanderlaan20
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Comment: C: What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
... Ah, so many thanks for these excellent answers and thoughts on this subject. So, now I understand a bit better the reason why people use t-SNE for single-cell RNA-seq: it's just to "better visualize the clustering / gene expression of particular gene" which makes perfect sense if you want certain gr ...
written 3 months ago by s.w.vanderlaan20
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What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
... Hi, I am curious why some papers and workflows (http://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html) using DESeq2 use PCA to cluster data to identify outliers in RNA-seq analyses. I've noticed that many single-cell RNA-seq experiments use tSNE to reduce data and visu ...
rnaseq deseq2 pca tsne written 4 months ago by s.w.vanderlaan20 • updated 4 months ago by Kushal K Dey10
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Comment: C: Error in loading GenomicMethylSet: "no slot of name 'elementMetadata' for this o
... I have the same issue. I created the object on the server and am now loading it in RStudio. `load(paste0(QC_loc,"/aems450k.RGChannelSetQC.Rdata"))` But apparently your trick won't work, as it won't be loaded at all... Any alternative, other then making the object from scratch...? ...
written 4 months ago by s.w.vanderlaan20
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Answer: A: Problem running dexseq in parallel using BiocParallel
... @Johannes Rainer Hi, What is your code exactly? I'm trying to do this:  SNOWPARAM <- SnowParam(snowWorkers(), type = "SOCK", progressbar = TRUE,   RNGseed = 9012014, log = TRUE, logdir = QC_loc, resultdir = QC_loc,   jobname = "QCAEMS450KCOMBO") When I do this afterwards: register(SNOW ...
written 7 months ago by s.w.vanderlaan20 • updated 7 months ago by Martin Morgan ♦♦ 20k

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Scholar 7 months ago, created an answer that has been accepted. For A: Problem running dexseq in parallel using BiocParallel

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