User: Lukas Chavez

gravatar for Lukas Chavez
Lukas Chavez470
Reputation:
470
Status:
Trusted
Location:
Germany
Last seen:
11 months, 3 weeks ago
Joined:
4 years, 9 months ago
Email:
l*******@dkfz.de

Posts by Lukas Chavez

<prev • 77 results • page 1 of 8 • next >
0
votes
2
answers
342
views
2
answers
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 5 months ago by Lukas Chavez470
0
votes
1
answers
143
views
1
answers
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 6 months ago by Lukas Chavez470
0
votes
1
answers
157
views
1
answers
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 7 months ago by Lukas Chavez470
0
votes
1
answers
198
views
1
answers
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 8 months ago by Lukas Chavez470
0
votes
1
answers
232
views
1
answers
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 10 months ago by Lukas Chavez470
0
votes
1
answers
198
views
1
answers
Answer: A: Insertion size when using 'paired' in MEDIPS.createSet()
... Dear Stine, the function getPairedGRange() contains the relevant interfaces to Rsamtools for importing bam files. These are: (...) scanFlag = scanBamFlag(isPaired = T, isProperPair = TRUE,             hasUnmappedMate = FALSE, isUnmappedQuery = F, isFirstMateRead = T,             isSecondMateRead = ...
written 11 months ago by Lukas Chavez470
0
votes
1
answers
333
views
1
answers
Answer: A: MEDIPS - do reads without CG's get filtered out prior to analysis?
... Dear Chu Shirly, no, reads without CpGs are not removed before calculating coverage. Only when calculating differential enrichment between conditions, windows without CpGs will not be tested, if the variable MeDIP is set to true. Please also consider our new package QSEA for the analysis of MeDIP- ...
written 13 months ago by Lukas Chavez470
0
votes
1
answers
181
views
1
answers
Answer: A: How does the 'paired' argument works in MeDIPS 1.23.2
... Dear Stine, thanks for your request. About 1) Yes, extend and shift is automatically ignored when MEDIPS is run in paired end mode. About 2) In paired end mode rpkm is in fact fpkm as the fragments are considered once. Abt 3) No, the second mate is not imported. However, the first mate has the i ...
written 14 months ago by Lukas Chavez470
0
votes
2
answers
342
views
2
answers
Comment: C: MeDIPS: warning when using "ttest" settings in MEDIPS.meth
... Dear Stine, thank you for sending additional information. I have to admit that I have not worked any more with the ttest functionality since we integrated the edgeR package. The difference in the total number of tested windows given the same minRowSum parameter is because it is applied to the coun ...
written 15 months ago by Lukas Chavez470
0
votes
1
answers
256
views
1
answers
Answer: A: Gene Symbol Annotation
... Hi Peter, I think its not possible to annotate DERs with gene symbols using the MEDIPS.annotate function. I recommend to use other tools available in R/Bioconductor for annotating genomic coordinates, such as ChIPpeakAnno, I have no experience with it but I think it can do the job? All the best, L ...
written 15 months ago by Lukas Chavez470

Latest awards to Lukas Chavez

Scholar 2.5 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?
Scholar 2.5 years ago, created an answer that has been accepted. For A: How createSet from reduced "paire-ed" sequencing on MeDIPS?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 122 users visited in the last hour