User: s.w.vanderlaan

Reputation:
40
Status:
New User
Location:
Netherlands
Website:
http://www.atheroexpre...
Twitter:
swvanderlaan
Last seen:
1 month, 3 weeks ago
Joined:
3 years, 11 months ago
Email:
s*************@gmail.com

Posts by s.w.vanderlaan

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to use 1000 Genomes data for LDheatmap package in R
... Did you ever fix this? ...
written 7 weeks ago by s.w.vanderlaan40
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Comment: C: LDheatmap with custom genome
... Did you ever fix this? ...
written 7 weeks ago by s.w.vanderlaan40
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What is the effect size in output of FaST-LMM when using EWASher?
... Hi, Perhaps a naive question, but it's just not clear to me. From the adapted FaST-LMM program EWASher I get this output. SNP Chromosome GeneticDistance Position Pvalue Qvalue N NullLogLike AltLogLike SnpWeight SnpWeightSE OddsRatio WaldStat NullBias NullCov00Weight NullCov01Weight ...
fast-lmm ewasher written 19 months ago by s.w.vanderlaan40 • updated 19 months ago by genomax62k
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Comment: C: Add GenomicRanges to SummarizedExperiment
... I did, here's what I get. > rowRanges(RAW_DESeq2A) > GRangesList object of length 63677: > $ENSG00000000003 > GRanges object with 0 ranges and 0 metadata columns: > seqnames ranges strand > > > $ENSG00000000005 > GRan ...
written 2.1 years ago by s.w.vanderlaan40 • updated 20 months ago by WouterDeCoster36k
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Comment: C: Add GenomicRanges to SummarizedExperiment
... I know. But the point is: these genomic ranges aren't present in my DESeq2 object. Like at all. So how do I get them in manually? ...
written 2.1 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.1 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.1 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.1 years ago by s.w.vanderlaan40
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Add GenomicRanges to SummarizedExperiment
... Hi, I've got RNAseq data which was processed and given to me in a text-file. The rows are EnsemblIDs, and the columns the individuals with their counts. I've loaded these data, and ran DESeq2. Now I want to plot the log2 fold changes similar as is explained here: http://www.bioconductor.org/help/w ...
deseq2 summarizedexperiment granges written 2.1 years ago by s.w.vanderlaan40 • updated 20 months ago by WouterDeCoster36k
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Answer: A: 450k CpG methylation to functional annotation
... Can't you just use the annotation file from Illumina? ...
written 2.9 years ago by s.w.vanderlaan40

Latest awards to s.w.vanderlaan

Popular Question 7 months ago, created a question with more than 1,000 views. For Add GenomicRanges to SummarizedExperiment
Popular Question 20 months ago, created a question with more than 1,000 views. For Correlation-heatmap alongside a protein level heatmap

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