User: s.w.vanderlaan

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Posts by s.w.vanderlaan

<prev • 12 results • page 1 of 2 • next >
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Answer: A: Merge column to SummarizedExperiment from other dataframe
... I think the issue is that the colData gets a different order than the Assay data, which should not happen. But if I sort = to the merge command everything is just fine, and I can add the colnames later on. So: dim(aems450k1.MvaluesQCIMPplaqueSE) aems450k1.MvaluesQCIMPplaqueSE colData(aems450k1.M ...
written 8 months ago by s.w.vanderlaan20
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Comment: C: Merge column to SummarizedExperiment from other dataframe
... I think the issue is that the colData gets a different order than the Assay data, which should not happen. But if I sort = to the merge command everything is just fine, and I can add the colnames later on. So: dim(aems450k1.MvaluesQCIMPplaqueSE) aems450k1.MvaluesQCIMPplaqueSE colData(aems450k1.M ...
written 8 months ago by s.w.vanderlaan20
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Merge column to SummarizedExperiment from other dataframe
... Hi, I have a RangedSummarizedExperiment which looks like this: class: RangedSummarizedExperiment&nbsp; dim: 483731 485&nbsp; metadata(4): creationDate author BBMRIomicsVersion note assays(1): data rownames(483731): cg01707559 cg02004872 ... ch.22.47579720R ch.22.48274842R rowData names( ...
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Comment: C: how to add a new column in colData in SummarizedExperiment
...   Hi, I have done the above, but using the merge function. See this post: https://stackoverflow.com/questions/52853688/merge-column-to-summarizedexperiment-from-other-dataframe.  How can I fix that I don't loose the colnames? Thanks ...
written 8 months ago by s.w.vanderlaan20
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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 22 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 23 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 23 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 23 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 24 months ago by s.w.vanderlaan20 • updated 24 months ago by Kushal K Dey10

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Popular Question 24 months ago, created a question with more than 1,000 views. For What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Problem running dexseq in parallel using BiocParallel

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