User: jrlarsen

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jrlarsen0
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Posts by jrlarsen

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Comment: C: Number of Probes per Segment for TCGA CNVs
... Thank you so much Kevin, your thesis does seem to address this issue. I would be happy to read your thesis, but maybe it’ll be a quicker read if this was applied in an article you published? I do enjoy a good Materials & Methods section haha ...
written 7 months ago by jrlarsen0
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Filtering number of markers after segmentation using DNAcopy
... I have copy number data from cancer patients, both cancer and matched normal, that have already been segmented using DNAcopy. The problem is the segmentation function in DNAcopy had min.width set to the default of 2 producing many segments with few markers that appear more like noise than signal. My ...
dnacopy copy number segmentation written 7 months ago by jrlarsen0 • updated 7 months ago by Eric T.2.5k
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Comment: C: Number of Probes per Segment for TCGA CNVs
... Hi Kevin, thank you for responding. Your link to the processing step really helped, and may require me to repost with a new question. I followed the link to the processing, then to the DNAcopy reference manual, and found the default command used by the TCGA for CBS (segmentation). It appears my ques ...
written 7 months ago by jrlarsen0
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Number of Probes per Segment for TCGA CNVs
... I am observing focal and broad events in CNVs found in the TCGA. I’ve noticed the post segmented CNV data has number of probes as low as 2, and produce segments that appear as possible noise (especially in normal profiles). I am curious if there is a minimum number of probes threshold, preferably ...
tcga cbs cnv written 7 months ago by jrlarsen0 • updated 6 months ago by Biostar ♦♦ 20
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Comment: C: Pruning CNA Data from TCGA
... This is extremely helpful,thank you! This is the first I have heard of GISTIC and looks like what I need. I cannot find a library for R that runs GISTIC, only via the terminal. Do you know any way to run it directly through R? R is the platform I am running everything through. Edit: Grammar ...
written 14 months ago by jrlarsen0
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Pruning CNA Data from TCGA
... Hello, I downloaded the CNA data from TCGA (GDC) which is pre-segmented by CBS using the DNAcopy library from Bioconductors (Level 3). I am currently analyzing the data but cannot find a way eliminate noise in the form of very short segments that do not match the surrounding segments of longer prob ...
tcgabiolinks dnacopy tcga cnv segmentation written 14 months ago by jrlarsen0 • updated 14 months ago by pbpanigrahi180

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