User: Günter Klambauer

Reputation:
540
Status:
Trusted
Location:
Austria
Website:
http://www.bioinf.jku....
Last seen:
1 month, 3 weeks ago
Joined:
6 years, 10 months ago
Email:
k********@bioinf.jku.at

Posts by Günter Klambauer

<prev • 88 results • page 1 of 9 • next >
2
votes
1
answer
103
views
1
answers
Answer: A: mosdepth output into cn.mops?
... Dear Philipp, Yes it is very well possible and also reasonable to use the output of mosdepth as input for cn.mops. There is only one thing to check: does mosdepth return "depth of coverage" or "readcounts"? From the GRanges object it seems that these are integer numbers and therefore read counts. ...
written 7 weeks ago by Günter Klambauer540
0
votes
2
answers
164
views
2
answers
Answer: C: tumor vs control: multiple samples
... Just use the default referencecn.mops function. Submit multiple tumor samples in the according input argument, and also multiple control samples in the according input argument. referencecn.mops will calculate an appropriate control sample and compare each tumor sample against the control.   ...
written 5 months ago by Günter Klambauer540
0
votes
3
answers
606
views
3
answers
Answer: A: cn.MOPs: Error in value[[3L]](cond) :
... Ok, this is a problem either with your BAM files or with Rsamtools with the function "scanBam". Please contact the maintainers of Rsamtools. ...
written 10 months ago by Günter Klambauer540
0
votes
3
answers
606
views
3
answers
Answer: A: cn.MOPs: Error in value[[3L]](cond) :
... I think this is not a problem of cn.mops but of an internally used function (Rsamtools?). Could you run "traceback" right after the error occurs and post the result here. Please check if for each BAM file, there exists an BAI (index) file. This can be generated using samtools Regards, Günter ...
written 10 months ago by Günter Klambauer540
1
vote
1
answer
229
views
1
answers
Answer: A: Doubt about WL in cn.mops
... Hi, This is an intrinsic problem of the read count data. If you have a small WL, the counts are low and you will easily get large fold-changes: Imagine that most samples of a readcount of 1 and one sample has a read count of 2. Then this would be a strong signal in terms of fold-changes (2-fold cha ...
written 10 months ago by Günter Klambauer540
1
vote
1
answer
229
views
1
answers
Comment: C: Doubt about WL in cn.mops
... see below   ...
written 10 months ago by Günter Klambauer540
0
votes
1
answer
221
views
1
answers
Answer: A: cn.mops: interpreting output when returnPosterior=TRUE
... 1. There is no additional column, but an extra slot (resCNMOPS@something) that returns the three dimensional array of posterior probs (segments x samples x copynumberclasses). 2. The default thresholds of cn.MOPS should work fine. If you have a validation set with known CNVs you should adjust the p ...
written 12 months ago by Günter Klambauer540
0
votes
1
answer
214
views
1
answers
Answer: A: best way to normalize for differences in sample read depth: normalize genome vs
... Hi, Yes, the function "cn.mops" internally also applies normalization. I just added the function "normalizeGenome" and "normalizeChromosome" for Users who want to normalize by hand. So, there is no difference between first applying the normalization function and then running cn.mops with "norm=0" ( ...
written 14 months ago by Günter Klambauer540
0
votes
1
answer
263
views
1
answers
Answer: A: Error with plotting with target sequencing data
... Hello, Thanks for using cn.mops. This error could also be related to the graphics devices. Could you please check if the error persist when you use other graphics devices (e.g. "pdf("tmp.pdf"); plot(resCNMOPS,which=5); dev.off()". If the error persists, please run "traceback()" directly after the e ...
written 15 months ago by Günter Klambauer540
0
votes
1
answer
328
views
1
answers
Comment: C: Error when use getSegmentReadCountsFromBAM
... Great, thanks for the heads-up!! ...
written 15 months ago by Günter Klambauer540

Latest awards to Günter Klambauer

Scholar 23 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 23 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 23 months ago, created an answer that has been accepted. For A: refSeqName issue in cn.MOPS
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Scholar 23 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.1 years ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: R code for cn.mops -- if a chromosome does not have CNV ?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.3 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.3 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 138 users visited in the last hour