User: Lukas Chavez

gravatar for Lukas Chavez
Lukas Chavez470
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470
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Trusted
Location:
USA/La Jolla/UCSD
Last seen:
6 months, 4 weeks ago
Joined:
5 years, 7 months ago
Email:
l**********@ucsd.edu

Posts by Lukas Chavez

<prev • 82 results • page 1 of 9 • next >
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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 4 months ago by Lukas Chavez470
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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 6 months ago by Lukas Chavez470
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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 6 months ago by Lukas Chavez470
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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 6 months ago by Lukas Chavez470
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Answer: A: RMS question in MEDIPS
... Hi enrique.yeh, thanks for sharing these results! I agree that rms values of the hyper-methylated samples should reflect the elevated signals you see by the rpkm values. Instead of looking at the mean values only, I am wondering how the genome wide distribution/ histogram of rms values compare betw ...
written 6 months ago by Lukas Chavez470
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Comment: C: MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Dear Stine, in case of the ttest, the minRowSum parameter is applied to the rpkm values instead of the counts. All the best, Lukas On 16. Jun 2017, at 15:49, stb [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support. ...
written 15 months ago by Lukas Chavez470
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Answer: A: Window size for MEDIPS
... Dear anupriyaverma1408, you can certainly try other window sizes such es 300 or 500nt. This will have a strong impact on the number of significant cases after correction for multiple testing as you are massively reducing the number of windows tested for differential enrichment. Due to the same reas ...
written 16 months ago by Lukas Chavez470
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Answer: A: How does the function MEDIPS.CpGenrich work?
... Dear Stine, it should always be the enrichment of CpGs within the sequencing data compared to the total number of sequenced DNA in a MeDIP experiment. This is compared to the relative abundance of CpGs in the reference genome and results in the enrichment score. Sincerely, Lukas On 27. Apr 2017, ...
written 17 months ago by Lukas Chavez470
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Answer: A: Error raised during execution of MEDIPS package
... Dear pinky_pinkpinky, please see my comments below. Sincerely, Lukas > On 1 Mar 2017, at 17:54, pinky_pinkpinky [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User pinky_pinkpinky wrote Question: Error raised duri ...
written 18 months ago by Lukas Chavez470
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Answer: A: MEDIPS: case study with different replicate numbers of control and case
... Dear Fei, comparisons of groups with different numbers of samples should not be a problem. You are referring to a different number of genomic regions tested for. Please create MEDIPS SETs or MEDIPSroiSets with the same parameter settings so that the resulting coverage vectors have the same length. ...
written 20 months ago by Lukas Chavez470

Latest awards to Lukas Chavez

Scholar 3.3 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?
Scholar 3.3 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?

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