User: yogacacarolom

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Brazil
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3 years, 7 months ago
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4 years, 9 months ago
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Posts by yogacacarolom

<prev • 16 results • page 1 of 2 • next >
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Obtaining LRR and BAF values from affymetrix SNP array
... I am trying to extract the `LRR` and `BAF` values from an affymetrix SNP chip without success using linux based tools. I tried to use a small subset in windows designed software called `Axiom™ CNV Summary Tools Software` and it works perfectly. The problem is that I have a huge dataset and would be ...
array cnv snp written 3.6 years ago by yogacacarolom60 • updated 3.5 years ago by soulsacross30
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Comment: C: Quantile normalization in huge matrices
... Yes, ff objects are as far I understand are hybrid objects and remain almost entirely on hard disk instead of RAM memory. The ff objects have several ff functions which mimetizes normal functions (mergeffdf, subsetffdf....), thats why I was wondering if this quantile normalize function could be adap ...
written 3.6 years ago by yogacacarolom60
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Quantile normalization in huge matrices
... I would like to apply the quantile normalization on a huge matrix. I tried to turn my matrix into a `ff` object as the example below: library(ff) df <- ' sample1 sample2 sample3 1834.2 1743.4 1384 4711 4922 4650 4555 1387 4650.8 ...
R big-data matrix written 3.6 years ago by yogacacarolom60
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Answer: A: PennCNV and segfault error
... I had the same problem and I solved installing a compatible perl version and replacing the first row of the 'detec_cnv.pl' function to especify my new perl version. ## INSTALL compatible version of perl with the perlbrew utility # install perlbrew \wget -O - http://install.perlbrew.pl | bash sourc ...
written 3.6 years ago by yogacacarolom60
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Obtaining LRR and BAF values from affymetrix SNP array
... I am trying to extract the `LRR` and `BAF` values from an affymetrix SNP chip without success using linux based tools. I tried to use a small subset in windows designed software called `Axiom™ CNV Summary Tools Software` and it works perfectly. The problem is that I have a huge dataset and would be ...
array R written 3.6 years ago by yogacacarolom60
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Binding several large matrices by column
... I truly know that 'large matrix issue' is a recurrent topic here, but I would like to explain minutely my specific problem regarding large matrices.    Strictly speaking, I want to `cbind` several large matrices with a specific name pattern in R. The below code shows my best try until this point. ...
R big-data matrix written 3.7 years ago by yogacacarolom60 • updated 3.7 years ago by Pierre Lindenbaum120k
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Comment: C: p.adjust with n < than number of tests
... Yes: "The idea of Meff-based approaches is simple: “filter out” the correlation among tests, leaving only the effective number of independent ones, Meff, and then use the Bonferroni or the Šidák correction by replacing M with Meff in the corresponding formula." (GAO et. al, 2010) -> http://www.nc ...
written 4.0 years ago by yogacacarolom60
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Comment: C: p.adjust with n < than number of tests
... I described more details about my analysis. Some idea of suitable strategy from now? ...
written 4.0 years ago by yogacacarolom60
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p.adjust with n < than number of tests
... I would like to apply the p.adjust  function in R where n is < number of p-values. The real number of independent tests is lower than the number of p-values as it cames from genomic data with Linkage Desequilibrium: However, the p.adjust function do not allows it: number of comparisons, must be ...
R bioconductor written 4.0 years ago by yogacacarolom60
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Comment: C: Changing the font size in autoplot and tracks functions
... Why it is not possible? This is not a ggplot2 based package? I really do not understand. ...
written 4.7 years ago by yogacacarolom60

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