User: Günter Klambauer

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Posts by Günter Klambauer

<prev • 53 results • page 1 of 6 • next >
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Comment: C: Call CNV in population with large depth variance
... Hello Xiao, The program determines the window length automatically based upon the sample with the lowest number of reads (lowest coverage). However, I advise to do some calculations and set this parameter by hand such that on average about 50-100 reads map to each window (segment). The average num ...
written 7 days ago by Günter Klambauer240
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Answer: A: Call CNV in population with large depth variance
... Hello Xiao Zhang, Yes, clustering the samples with respect to sequencing depth is certainly advisable. You can include the higher coverage samples when you analyze the low coverage ones. Let me explain this further: Let's say the low coverage samples are A, the medium coverage samples are B, and th ...
written 7 days ago by Günter Klambauer240
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Comment: C: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hello Amal, There is a workaround: Go back to the initial "getReadCountsFromBAM" and use a small segment size, e.g. "WL=50". Then you get a read count matrix with segments/windows along the whole genome. Remove rows with zero read counts across all samples (these are the DNA segments that were not ...
written 8 days ago by Günter Klambauer240
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Answer: A: How to use cn.mops to detect CNVs from Targeted DNA Sequencing data?
... Hello Amal, The reason for this behaviour of cn.mops is that you used the "whole genome sequencing" script. The function "getReadCountsFromBAM" partitions the genome into equally sized windows and counts how many reads are in these windows. However, you have targeted sequencing data and you should ...
written 10 days ago by Günter Klambauer240
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Answer: A: Input (X) data type is not numeric if read from GRanges obj
... Hello Mohammad, Your comments are very welcome - as always! Thanks for flagging this issue. I will make the changes to cn.mops accordingly. Regards, Günter On 2016-12-28 07:20, Mohammad Alkhamis [bioc] wrote: > Activity on a post you are following on support.bioconductor.org > <https: ...
written 22 days ago by Günter Klambauer240
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Answer: A: cn.mops: NA in the output of referencecn.mops
... Hello Radek, Thanks for using cn.mops! This functionality should actually work. The return object should contain the integer copy numbers of the cases. Could you please upgrade to the most recent version of R / Bioconductor / cn.mops and check if the problem persists? If yes, could you give me ...
written 8 weeks ago by Günter Klambauer240
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Answer: A: about cn.MOPS: paired vs unpaired
... Hello Bogdan, Thanks for using cn.mops. Yes, this refers to "paired-end reads" or "single-end reads"! Parallelization is implemented, you can simply set the parameter "parallel=4" of "getReadCountsFromBAM" or "cn.mops" and the code will be executed on 4 cores. The only thing that is necessary f ...
written 10 weeks ago by Günter Klambauer240
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Answer: A: Suggestion: type of ExpLogFoldChange (sini)
... Hello Mohammed, Thanks for looking into cn.mops so closely. The suggested changes make sense. I have just committed them to the development branch (they should appear in version 1.21.1 shortly). Regards, Günter ...
written 3 months ago by Günter Klambauer240
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Answer: A: No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
... Hello, Can you please run "traceback()" right after the error happens and post the result. I suspect that this is not a cn.MOPS error...   Regards, Günter ...
written 4 months ago by Günter Klambauer240
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Answer: A: No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
... Hello Ponyo,   Thanks for your question. This is actually not an error message, this just means that there were no CNVs detected. The fact that even after changing the hyperparameters, such as "priorImpact", there are not detections means that cn.MOPS provided robust results. In other words, there ...
written 4 months ago by Günter Klambauer240

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 12 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 12 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 18 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package
Scholar 18 months ago, created an answer that has been accepted. For A: Adjusting the defaults in the cn.MOPs Package

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