User: Matthias Lienhard

Reputation:
120
Status:
Trusted
Location:
Max Planck Institute for molecular Genetics, Berlin, Germany
Website:
http://www.molgen.mpg....
Scholar ID:
Google Scholar Page
Last seen:
1 month ago
Joined:
3 years, 6 months ago
Email:
l*******@molgen.mpg.de

Education

  • 2008: Bachelor of Science in Bioinformatics, FU Berlin (Germany)
  • 2011: Master of Science in Bioinformatics, FU Berlin
  • Since 2012: PhD studies at the IMPRS-CBSC supervised by Dr. Ralf Herwig

 

Posts by Matthias Lienhard

<prev • 14 results • page 1 of 2 • next >
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Comment: C: CNV parameter not working - MEDIPS
... Unfortunately, MEDIPS.getAnnotation does not fetch gene names, and the function cannot be configured, such that it does fetch them. You could either modify the function, or match the ids and change the resulting output tables manually. ...
written 5 weeks ago by Matthias Lienhard120
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Comment: C: CNV parameter not working - MEDIPS
... Hi Anupriya, within MEDIPS, the calculation of CNV works by comparing the local coverage of the input sample(s)  that contain CNVs (ISet2) to the control input sample(s) (ISet1). Therefore it is required to specify both sets. However, probably the read coverage is not sufficient to run the CNV det ...
written 5 weeks ago by Matthias Lienhard120
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Answer: A: CNV parameter not working - MEDIPS
... Hi Anupriya Verma, MEDIPS.createSet calculates CNVs based on the window size selected for the primary MeDIP seq analysis. In most cases, the input coverage is not sufficient for CNV detection at this resolution. Maybe, that this somehow leads to the error message you got. The suggested way would be ...
written 6 weeks ago by Matthias Lienhard120
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Answer: A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
... Hi Justin, I used two perl script to summarize the TCGA data into genome wide bins: 1) SummarizeTables.pl combines several sample files in a single table. 2) summarize_bs_in_bins.pl sumerizes bisulfite values in genome wide bins of fixed size by computing the average % methylation values. I prov ...
written 11 weeks ago by Matthias Lienhard120
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Comment: C: Alternative methylation contexts with MEDIPS?
... Hi Chris, maybe I wasn't clear, what I ment was the following behavior of matchPattern, when setting fixed=F >library(BSgenome.Hsapiens.UCSC.hg19) >library(Biostrings) >chr_seq=getBSgenome("BSgenome.Hsapiens.UCSC.hg19")[["chr1"]] >chr_seq   249250621-letter "DNAString" instance seq: N ...
written 10 months ago by Matthias Lienhard120
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Answer: A: Alternative methylation contexts with MEDIPS?
... Hi Chris, I recently developed qsea, an alternative package for the analysis of enrichment based methylation data, which is in the currently in the devel-branch of Bioconductor. The package is based on the ideas of MEDIPS, but extends the functionality and facilitates the usage. The focus is on est ...
written 10 months ago by Matthias Lienhard120
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Comment: C: New to R: How to use your own data for Bioconductor Packages
... Hi hseepany, can you please specify what exactly you want to do, what commands you tried to apply, and the error message you received. ...
written 22 months ago by Matthias Lienhard120
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SssI free analysis in BayMeth/Repitools
... Hello Repitools developers, I am trying to obtain % methylation values from MeDIP samples where I do not have SssI control using BayMeth, but I fail at the first step: the creation of a BayMethList object. This function results in an error if no control is provided. I found no examples of a SssI fr ...
repitools written 23 months ago by Matthias Lienhard120
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Answer: A: Non-CpG Methylation in MEDIPS Package
... Dear Marc, as Lukas pointed out, MeDIP seq (or any other mC enrichment based methylation assay) is not well suited to distinguish between CpG and CpN methylation. However, you can use MEDIPS to judge whether there is a substantial fraction of non CpG methylation by looking at the calibration plots: ...
written 2.3 years ago by Matthias Lienhard120
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Answer: A: mr.edgeR tests in MEDIPS package
... Hi Kelly, the CSet is used for CpG dependent normalization ("rms" and "prob") only, and does not effect the differential coverage test results (logFC, pvalue ...) calculated by edgeR. To avoid confusion, you could set MeDIP to FALSE, then the CpG normalized values are not calculated. Best, Matthia ...
written 3.1 years ago by Matthias Lienhard120

Latest awards to Matthias Lienhard

Scholar 11 weeks ago, created an answer that has been accepted. For A: Generation of QSEA TCGA 450K Human Methylation Calibration Dataset
Autobiographer 2.7 years ago, has more than 80 characters in the information field of the user's profile.

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