User: Lukas Chavez

gravatar for Lukas Chavez
Lukas Chavez510
Reputation:
510
Status:
Trusted
Location:
USA/La Jolla/UCSD
Last seen:
1 year, 3 months ago
Joined:
6 years, 3 months ago
Email:
l**********@ucsd.edu

Posts by Lukas Chavez

<prev • 88 results • page 1 of 9 • next >
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Answer: A: sva correction for MEDIPS
... Dear Kaj, sva normalization is not available in MEDIPS. The diffnorm parameter allows to perform umm or quantile normalization prior to calculating differential enrichment. All the best, ...
written 3 months ago by Lukas Chavez510
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Answer: A: Comparing more than 2 experimental groups with MEDIPS?
... Dear mtefit, MEDIPS does not allow to analyze multiple (>2) conditions. Please consider our R/BioC package qsea, which also has MeDIP-seq specific functionalities but also allows the use of a design matrix. Sincerely, Lukas _____________________________________ Lukas Chavez, Ph.D. Assistant Pr ...
written 5 months ago by Lukas Chavez510
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Answer: A: create.set on MEDIPS
... Hi Oussama, Have you successfully loaded the BSgenome such as library(BSgenome.Oeuropaea.IOGC.v1)? Best, Lukas On Nov 14, 2018, at 3:29 PM, oussama.badad [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.biocond ...
written 6 months ago by Lukas Chavez510
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Comment: C: CpG density in MEDIPS
... Hi Gautam, Please see pages 14-15 of the Reference Manual for a description of the values returned by the MEDIPS.meth function (including the counts and log fold change values). Please let me know in case you have further questions. All the best, Lukas _____________________________________ Lukas Ch ...
written 7 months ago by Lukas Chavez510
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Answer: A: CpG density in MEDIPS
... Hi Gautam, The bam counts for each window do not give you information about the number of CpGs in that window. All the best, Lukas _____________________________________ Lukas Chavez, Ph.D. Assistant Professor, Department of Medicine University of California, San Diego (UCSD) Biomedical Research F ...
written 7 months ago by Lukas Chavez510
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Answer: A: Coupling set error in MEDIPS
... Hi Gautam, If you are interested in differential methylation between conditions you do not necessarily need CpG density normalization. I do not see a reason why this should be different in plants. For estimates of % DNA methylation I recommend the QSEA package, All the best, Lukas _______________ ...
written 7 months ago by Lukas Chavez510
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Answer: A: MEDIPS - Annotation output explanation
... Hi Vjain, My query is - 1. How to analyse this result? You table contains a list of potentially differentially enriched regions. What exactly this is and how you want to further analyze depends on your research question 2. How to get exact position of chromosome ? Please see columns chr | star ...
written 12 months ago by Lukas Chavez510
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Comment: C: MEDIP: Problem with MEDIPS.createSet
... Hi Vjain, The chromosome names of your custom genome might not match the chromosome names of your sequencing reads? See for example this previous question: MEDIPS.createSet error Lukas On Mar 21, 2018, at 3:33 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> ...
written 14 months ago by Lukas Chavez510
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Comment: C: MEDIP: Problem with MEDIPS.createSet
... Hi Vjain, Would you please share your solution to your error? For the new error: it seems as if you try to access a subset of Set1 by Set1[[1]] even though there are no subsets. Have you simply tried refObj = Set1 ? Best, Lukas On Mar 20, 2018, at 2:51 AM, vjain [bioc] <noreply@bioconductor. ...
written 14 months ago by Lukas Chavez510
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Answer: A: MEDIP: Problem with MEDIPS.createSet
... Hi Vjain, MEDIPS expects a bam file like file=“/path/to/file.bam”. Please do not specify a preprocessed bam file object. All the best, Lukas On Mar 19, 2018, at 2:27 AM, vjain [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are followi ...
written 14 months ago by Lukas Chavez510

Latest awards to Lukas Chavez

Scholar 4.0 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?
Scholar 4.0 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?

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