User: Sandro Morganella

Reputation:
30
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New User
Location:
United Kingdom
Last seen:
3 years, 4 months ago
Joined:
4 years, 1 month ago
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m************@gmail.com

Posts by Sandro Morganella

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Comment: C: Gaia not returning results - load_cnv problem
... I have double checked and the problem reported here is actually related to the fact that the probes inside the markersMatrix does not contain all the probes reported in the cnvMatrix. Note that the markersMatrix must have a probe for each Start and End reported in the cnvMatrix. You have two option ...
written 11 months ago by Sandro Morganella30
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Comment: C: Gaia not returning results - load_cnv problem
... The is related to the cnvMatrix: the colulmn 'Num.of.Markers' must report the size of the aberrant region (End-Start). I can see that the manual/help is misleading in calling this Num.of.Markers, it should be 'Region Size' (or something like that). I need to fix this problem with the manual/help. ...
written 11 months ago by Sandro Morganella30
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Comment: C: Gaia not returning results - load_cnv problem
... How I said it is quite hard for me to understand where the problem is without looking at the data. Anyway, If you could send me the data for chr1 (both cnv and probe data) I will try to understand how to fix the issue. Please use this email morganellaalx [at] gmail.com On Wed, Aug 15, 2018 at 11:05 ...
written 11 months ago by Sandro Morganella30
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Comment: C: Gaia not returning results - load_cnv problem
... As last attempt, could you try to run the analysis only on the probes/cnv of chromosome 1? On Mon, Aug 13, 2018 at 8:38 PM, rina [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rina <https: support.bioconductor. ...
written 11 months ago by Sandro Morganella30
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Comment: C: Gaia not returning results - load_cnv problem
... Are the positions of the probes in your markers matrix consistent with the cnv matrix? It is quite hard for me to understand what is the problem without looking at data. On Mon, Aug 13, 2018 at 2:17 PM, rina [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following ...
written 11 months ago by Sandro Morganella30
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Answer: A: Gaia not returning results - load_cnv problem
... Hi, I think the issue can be related to the order of your matrix. Try to order your matrix so that the sample name is in the first column. In particular your matrix should have exactly this format: $ Sample.Name $ Chromosome $ Start $ End. $ Num.of.Markers $ Aberration The function that loads the ...
written 11 months ago by Sandro Morganella30
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Comment: C: Gaia results including negative widths
... No problem, I'm glad it works now. On Thu, Aug 9, 2018 at 9:34 PM, Talip Zengin [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User Talip Zengin <https: support.bioconductor.org="" u="" 14290=""/> wrote Comment: ...
written 11 months ago by Sandro Morganella30
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Answer: A: Gaia results including negative widths
... Hi Talip, The probe positions must be sorted by their genomic position. Sorting the probes will fix your problem. Best, Sandro On Thu, Aug 9, 2018 at 3:23 PM, Talip Zengin [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > ...
written 11 months ago by Sandro Morganella30
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Comment: C: GAIA package Error: cannot allocate vector of size 852.1 Mb
... In order to use gaia on this dataset you need to increase R memory limit. Here some useful information: https://stat.ethz.ch/R-manual/R-devel/library/base/html/Memory-limits.html On Fri, Dec 1, 2017 at 1:20 PM, drusmanbashir [bioc] < noreply@bioconductor.org> wrote: > Activity on a pos ...
written 19 months ago by Sandro Morganella30
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Answer: A: GAIA package Error: cannot allocate vector of size 852.1 Mb
... Hi, From your log I can deduce that it is actually a problem related to the memory. In order to double check this, you can try to run GAIA on a subset of your data (i.e., reduce either the number of probes or the number of samples). Best, Sandro On Fri, Dec 1, 2017 at 12:43 PM, drusmanbashir [b ...
written 19 months ago by Sandro Morganella30

Latest awards to Sandro Morganella

Scholar 3.3 years ago, created an answer that has been accepted. For A: Gaia results including negative widths

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