User: John Blischak

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John Blischak140
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Posts by John Blischak

<prev • 6 results • page 1 of 1 • next >
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Answer: A: export funciton alters ranges in output BED file
... Hi Dolev, On Sun, Sep 14, 2014 at 9:42 AM, do r wrote: > However, the ranges in the output file are altered so that the start > coordinate is subtracted by one, > > Since I intend to later to searrch for intersections between the > ranges in the BED file and variants in a vcf file ( ...
written 3.7 years ago by John Blischak140
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Answer: A: Biomart annotation
... Hi, I don't think there is a problem. Ensembl includes annotations for some genes that Entrez does not. An example that I found using the code below, RN7SL163P is a pseudogene included in Ensembl (ENSG00000266195) but not in Entrez. If you are not interested in pseudogenes, this should not be an is ...
written 3.9 years ago by John Blischak140
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Comment: C: using duplicateCorrelation with limma+voom for RNA-seq data
... Thanks for the feedback Bernd and Ryan. > Now it can well be that it does not really matter for the computed weights > whether the correlation is > taken into account or not (as your example seem to indicate) so a second > run of voom might not be necessary but I would always do it sinc ...
written 4.0 years ago by John Blischak140 • updated 3.0 years ago by Gordon Smyth33k
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Answer: A: Package qvalue - can it be installed without TCL-TK support?
... A short-term solution would be to download the source code and just directly use the qvalue function. wget http://bioconductor.org/packages/release/bioc/src/contrib/qvalue_1.38. 0.tar.gz tar xzf qvalue_1.38.0.tar.gz Then source the code in R: source("qvalue/R/qvalue.R") If you wanted to install ...
written 4.0 years ago by John Blischak140
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using duplicateCorrelation with limma+voom for RNA-seq data
... Hi, I would like to use the duplicateCorrelation function along with limma and voom in order to analyze some RNA-seq data with blocking and group-means parametrization (similar to example 9.7 in the limma manual). The manual does not contain a similar example using the voom function for RNA-seq dat ...
limma voom written 4.0 years ago by John Blischak140 • updated 3.0 years ago by Gordon Smyth33k
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Comment: C: QQ plot 450k data
... Hi all, I think this depends on what question Khadeeja wants to answer. Traditionally a qqplot of the p-values from many statistical tests is used to assess the amount of signal in the data, i.e. low p-values (though this could be due either to true biological signal or biases). I assume this is wh ...
written 4.0 years ago by John Blischak140

Latest awards to John Blischak

Good Question 11 months ago, asked a question that was upvoted at least 5 times. For using duplicateCorrelation with limma+voom for RNA-seq data
Appreciated 3.7 years ago, created a post with more than 5 votes. For using duplicateCorrelation with limma+voom for RNA-seq data
Popular Question 3.7 years ago, created a question with more than 1,000 views. For using duplicateCorrelation with limma+voom for RNA-seq data
Student 3.7 years ago, asked a question with at least 3 up-votes. For using duplicateCorrelation with limma+voom for RNA-seq data

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