User: Günter Klambauer

Reputation:
490
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Trusted
Location:
Austria
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http://www.bioinf.jku....
Last seen:
1 month, 2 weeks ago
Joined:
5 years, 10 months ago
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Posts by Günter Klambauer

<prev • 82 results • page 1 of 9 • next >
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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 6 weeks ago by Günter Klambauer490
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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 12 weeks ago by Günter Klambauer490
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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 4 months ago by Günter Klambauer490
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Comment: C: Error when use getSegmentReadCountsFromBAM
... Great, thanks for the heads-up!! ...
written 4 months ago by Günter Klambauer490
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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 4 months ago by Günter Klambauer490
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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 4 months ago by Günter Klambauer490
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Answer: A: Error when use getSegmentReadCountsFromBAM
... Hi, Can you please run "scanBamHeader" (or similar command) from Rsamtools and check the sequence names in the resulting object? Please let me know the results. Regards, Günter ...
written 4 months ago by Günter Klambauer490
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Answer: A: Cn.mops error: Error in if (sum(rds.counts) == 0) { : missing value where TR
... Hello Jieqiong Dai, It is really hard to diagnose the problems but it seems that the "getReadCountsFromBAM" function does not find any reads in your BAM files. Have you tried setting the parameter "mode" to "paired" or "unpaired"? Have you upgraded cn.mops and R to the latest version? Do your BAM f ...
written 5 months ago by Günter Klambauer490
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Answer: A: cn.MOPs issue with "Error in if (all(segMedianT == 0))"
... There seems to be some problem with the read counts. Can you check the distributions of read counts (the values in your object "bDR"), such as mean, median, max, number of zeros, NAs? ...
written 6 months ago by Günter Klambauer490
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Comment: C: Is cn.mops can be used for detecting CNV for targeted sequencing of 8M region
... Hello, For good performance you would need eight high quality samples, but if you only have 2 then you can still try it out -- after all, it is the best thing you can do and the alternative would be to not analyse the data. Note, that the performance estimates that we give in our paper will not hol ...
written 6 months ago by Günter Klambauer490

Latest awards to Günter Klambauer

Scholar 11 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 11 months ago, created an answer that has been accepted. For A: Finding structural analogs with Rchemcpp
Scholar 11 months ago, created an answer that has been accepted. For A: refSeqName issue in cn.MOPS
Teacher 11 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 12 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 12 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
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: R code for 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 ?
Scholar 13 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.4 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.4 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 2.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 2.9 years ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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