User: Günter Klambauer

Reputation:
510
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Trusted
Location:
Austria
Website:
http://www.bioinf.jku....
Last seen:
1 month ago
Joined:
6 years ago
Email:
k********@bioinf.jku.at

Posts by Günter Klambauer

<prev • 86 results • page 1 of 9 • next >
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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 5 weeks ago by Günter Klambauer510
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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 5 weeks ago by Günter Klambauer510
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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 6 weeks ago by Günter Klambauer510
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Comment: C: Doubt about WL in cn.mops
... see below   ...
written 6 weeks ago by Günter Klambauer510
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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 3 months ago by Günter Klambauer510
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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 4 months ago by Günter Klambauer510
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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 6 months ago by Günter Klambauer510
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Great, thanks for the heads-up!! ...
written 6 months ago by Günter Klambauer510
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Can you please run "traceback()" directly after the error occurs and post it here? ...
written 6 months ago by Günter Klambauer510
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Seems like the sequence names are "chr19_42791865_42792021_CIC" rather than "chr19", that's why the function does not find any reads. Please check why this happens in your BAM file. ...
written 6 months ago by Günter Klambauer510

Latest awards to Günter Klambauer

Scholar 13 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 13 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 13 months ago, created an answer that has been accepted. For A: refSeqName issue in cn.MOPS
Teacher 13 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 14 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 14 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 15 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: R code for cn.mops
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.5 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.5 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.6 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.6 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.1 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 3.1 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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