User: s.w.vanderlaan

Reputation:
20
Status:
New User
Location:
Last seen:
1 month, 4 weeks ago
Joined:
1 year, 8 months ago
Email:
s*************@gmail.com

Posts by s.w.vanderlaan

<prev • 12 results • page 1 of 2 • next >
0
votes
2
answers
109
views
2
answers
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 weeks ago by s.w.vanderlaan20
0
votes
2
answers
109
views
2
answers
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 weeks ago by s.w.vanderlaan20
0
votes
2
answers
109
views
2
answers
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( ...
0
votes
1
answers
288
views
1
answers
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 weeks ago by s.w.vanderlaan20
0
votes
0
answers
444
views
0
answers
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 ...
0
votes
2
answers
2.3k
views
2
answers
Comment: C: Standard error and effect size from Limma
... Ah, thank you for the answer, this was not immediately clear to me.   ...
written 16 months ago by s.w.vanderlaan20
0
votes
2
answers
2.3k
views
2
answers
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 16 months ago by s.w.vanderlaan20
0
votes
2
answers
2.3k
views
2
answers
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 16 months ago by s.w.vanderlaan20
0
votes
2
answers
4.1k
views
2
answers
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 16 months ago by s.w.vanderlaan20
9
votes
2
answers
4.1k
views
5 follow
2
answers
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 17 months ago by s.w.vanderlaan20 • updated 17 months ago by Kushal K Dey10

Latest awards to s.w.vanderlaan

Popular Question 17 months ago, created a question with more than 1,000 views. For What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
Scholar 20 months ago, created an answer that has been accepted. For A: Problem running dexseq in parallel using BiocParallel

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 142 users visited in the last hour