User: twtoal

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twtoal0
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Posts by twtoal

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Comment: C: PureCN: Error in plot.window(...) : need finite 'ylim' values
... Could PureCN be getting some NA values somehow for plotting, and accidentally generating an NA value for ylim?   ...
written 21 days ago by twtoal0
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PureCN: Error in plot.window(...) : need finite 'ylim' values
... I'm running PureCN (developer version 1.11.8) on a new project, and a number of errors occur, one of which is: INFO [2018-06-20 13:46:48] Done. INFO [2018-06-20 13:46:48] ------------------------------------------------------------ INFO [2018-06-20 13:46:48] Fitting variants for purity 0.39, tum ...
purecn written 24 days ago by twtoal0
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PureCN Error in xg[1, ] : incorrect number of dimensions
...   I'm running PureCN (development version V1.11.8) on a new project for the first time, and some errors occur, one of which is: WARN [2018-06-20 13:37:46] Could not impute mapping bias for all variants. Did you use calculateMappingBiasVcf? INFO [2018-06-20 13:37:46] Sample sex: F INFO [2018-06- ...
purecn written 24 days ago by twtoal0
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Comment: C: Unable to find solution: low coverage
... No, I did not use such a FASTA.  Just checked it and repeats aren't masked.  Can you give me an exact position where you see such 0 mappability that shouldn't be 0? I wonder if this is something to do with the new GEM mappability program version that I used.  When examining my old and new mappabili ...
written 6 weeks ago by twtoal0
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Comment: C: Is mean adjusted for purity?
... Your equation matches the one in the paper you cited, which I believe is incorrect.  Look at his preceding equations.  He says R'(x) = q(x)/T, which is as one would expect.  If you then plug in his equation for q(x), and in that equation replace D with his equation relating D to alpha and tau, you g ...
written 6 weeks ago by twtoal0
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Comment: C: Is mean adjusted for purity?
... Thanks, that was a helpful reference.  However, I see that it has a mistake in its equation for R'(x).  I believe the correct equation should be: R'(x) = q(x)/T = [atR(x) + 2(1-a)R(x) - 2(1-a)] / aT T = tau, a = alpha, q(x) = integer CN in cancer cells, R(x) = observed CN ratio, R'(x) = CN ratio i ...
written 6 weeks ago by twtoal0
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Is mean adjusted for purity?
... You previously indicated that the C values in the PureCN output have been adjusted for purity.  Does this also hold true for the "mean" values for mean log ratios?  It appears to me that they are adjusted for purity (but are still log mean ratios, not actual mean ratios and not twice the ratio to gi ...
purecn mean ratio written 6 weeks ago by twtoal0 • updated 6 weeks ago by markus.riester90
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Comment: C: Unable to find solution: low coverage
...     No, I used --offtargetwidth=200000 where 200000 is the default value you documented for --offtargetwidth. I did generate a new mappability file using a new version of GEM sent to me by Paolo Ribeca, which he said fixed problems with the version you used.  I ran it with the same parameters you ...
written 6 weeks ago by twtoal0
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Is C adjusted for purity?
... Several PureCN output files have "C" columns containing estimated copy number.  Is the data in these columns adjusted for purity?  That is, do they reflect the copy number of the tumor tissue and not the normal tissue that is mixed in with it?  If not, am I correct to think that the adjustment would ...
purecn adjusted c written 7 weeks ago by twtoal0 • updated 7 weeks ago by markus.riester90
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Comment: C: Unable to find solution: low coverage
... For CH59-T1, PureCN indicates a coverage of around 50X, which matches my own data, and PureCN estimates duplication around 20%, which doesn't seem too high.  The coverage is lower than most of our other samples, and we are planning to get more sequencing data, but I wouldn't call that coverage extre ...
written 7 weeks ago by twtoal0

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