User: m.van_iterson

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Netherlands
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1 month, 2 weeks ago
Joined:
2 years, 5 months ago
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Posts by m.van_iterson

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Parallel reading of Vcfs using VcfStack/RangedVcfStack
... Thanks that would be really nice! ...
written 6 months ago by m.van_iterson20
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Parallel reading of Vcfs using VcfStack/RangedVcfStack
... I really appreciate the latest addition to GenomicFiles VcfStack for handling a collection of vcfs, very convenient! However, I could not find any documentation to extract information from the vcfstack in parallel, i.e. using the assay-method. By looking at the source code I noticed this function i ...
biocparallel genomicfiles written 6 months ago by m.van_iterson20 • updated 4 months ago by shepherl ♦♦ 510
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Answer: A: How to control p-value inflation with limma
... Dear Stephane, I wouldn't not use bacon for this. bacon is really meant for association studies with sample size n>100. Also I wouldn't not use the GWAS inflation factor it is really meant for GWAS data. Did you check the limma userguide there is a whole chapter devoted to single channel arrays ...
written 8 months ago by m.van_iterson20
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Answer: A: Problem reading EPIC array data: different bead locations on different EPIC Chip
... Dear Kasper, Thanks for the explanation! Cheers, Maarten     ...
written 16 months ago by m.van_iterson20
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Problem reading EPIC array data: different bead locations on different EPIC Chips
... Dear list, I came across a specific issue when reading Illumina DNA Methylation EPIC data using minfi/illuminaio. Which I could trace down to the problem of different bead locations on different chips (see output below). This has consequences for reading data using minfi (and probably other package ...
minfi illuminaio epic written 16 months ago by m.van_iterson20
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News: Announcement of a new package called bacon
... Dear all, I would like to introduce the package bacon that has been added to bioconductor just before the release of version 3.3. bacon can be used to estimate and control for bias and inflation often present in epigenome- and transcriptome-wide association studies(EWAS/TWAS). The idea behind baco ...
news software r written 17 months ago by m.van_iterson20
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Answer: A: getting sample size for RNAseq experiment
... Dear Roser, You are planning to do many tests (some of which are two-sample tests) each test will have it's own power. If I understand correctly you want to do a power and sample size analysis for all tests at once? I do not know a proper way to do this. I can image that you do a power and sample s ...
written 21 months ago by m.van_iterson20
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Answer: A: getting sample size for RNAseq experiment
... Could you exactly formulate the hypotheses you want to test, e.g. for biopsy I is there any difference between the samples at time point t1 compared to time point t2 or so? Did you looked at the limma userguide section 9.6 Time Course Experiments? Cheers, Maarten ...
written 21 months ago by m.van_iterson20
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Answer: A: getting sample size for RNAseq experiment
... Dear Roser, The SSPA package can do power and sample size analysis for RNAseq data using test-statistics other then t-test statistics for two-group comparison.  For example, see the vignette for a chi-square example or our paper for F-statistics example. It's not completely clear to me which test ...
written 21 months ago by m.van_iterson20
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Answer: A: Trouble understanding how to load my idat files into MethylAid.
... Hi Julian, To use MethylAid you first have to create a targets file e.g. "targets.csv". This file contains the sample description, for example, a column with Sample_Names, the Sample_Wells and Sample_Plates etc. Usually, such a file is also provided by the data generation centre. You should add a c ...
written 2.1 years ago by m.van_iterson20

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