User: Lukas Chavez

gravatar for Lukas Chavez
Lukas Chavez470
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470
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Location:
USA/La Jolla/UCSD
Last seen:
8 months, 3 weeks ago
Joined:
5 years, 8 months ago
Email:
l**********@ucsd.edu

Posts by Lukas Chavez

<prev • 85 results • page 1 of 9 • next >
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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 25 days ago by Lukas Chavez470
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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 25 days ago by Lukas Chavez470
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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 4 weeks ago by Lukas Chavez470
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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 6 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 7 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 7 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 7 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 8 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 17 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 18 months ago by Lukas Chavez470

Latest awards to Lukas Chavez

Scholar 3.5 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?
Scholar 3.5 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?

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