User: Brent Pedersen

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Posts by Brent Pedersen

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Comment: C: sva::ComBat without covariate of interest?
... Here is the change that introduced this: https://github.com/jtleek/sva-devel/commit/bdae45f74f6ef2d507939dc840cc17e78fb0a631   ...
written 4.8 years ago by Brent Pedersen90
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sva::ComBat without covariate of interest?
... Older versions of the SVA manual suggest to include the covariate of interest in the model when running ComBat -- e.g. 'cancer' in this manual: http://bioconductor.org/packages/2.9/bioc/vignettes/sva/inst/doc/sva.pdf The devel and release versions: http://bioconductor.org/packages/release/bioc/vign ...
sva combat written 4.8 years ago by Brent Pedersen90 • updated 4.8 years ago by W. Evan Johnson800
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Comment: C: Analyzing "differential variability" of methylation (and gene expression)
... This was for charm data: http://biostatistics.oxfordjournals.org/content/13/1/166 but could be a starting point after adjusting for cell-types? As implemented (http://biostat.jhsph.edu/~ajaffe/code/vmrFinder.R) , it only allows for dichotomous covariate. On Fri, May 10, 2013 at 8:59 AM, Simone wro ...
written 6.4 years ago by Brent Pedersen90
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Comment: C: Gviz DataTrack, type="densityplot"
... On Thu, Nov 15, 2012 at 1:27 AM, Hahne, Florian wrote: > Hi Brent, > There is no particular reason why density plots are nor a standard plot > type in Gviz. I guess my reasoning was that those would not be necessary > because the only real application that I see here is for data smoothi ...
written 6.8 years ago by Brent Pedersen90
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Gviz DataTrack, type="densityplot"
... Hi, I have been using Gviz to plot some of our methylation data. It is very easy to make detailed figures. I had been plotting the methylation of case vs. control using DataTrack with groups and type="boxplot". I also tried an AnnotationTrack with fun=details, where details is essentially identical ...
gviz written 6.8 years ago by Brent Pedersen90 • updated 6.8 years ago by florian.hahne@novartis.com1.6k
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recourse for errors with GEOquery::getGEO
... Hi, with a call like > getGEO("GSE15219", destdir="/tmp/", GSEMatrix=TRUE) I get: Found 1 file(s) GSE15219_series_matrix.txt.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 762k 10 ...
written 6.9 years ago by Brent Pedersen90 • updated 6.9 years ago by Sean Davis21k
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Answer: A: Variance stabilization of m-values
... On Thu, Aug 2, 2012 at 5:19 PM, Gordon K Smyth wrote: > Use eBayes with trend=TRUE later in the pipeline, then variance > stabilization may not be needed. > > Gordon Is that recommendation only for beta values? when using M-values as a matrix, fit$Amean is not set so this gives an err ...
written 7.1 years ago by Brent Pedersen90
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Comment: C: Question about interpretation of CHARM results
... On Mon, Aug 20, 2012 at 12:28 PM, Tim Triche, Jr. wrote: > > > On Mon, Aug 20, 2012 at 10:42 AM, Brent Pedersen wrote: >> >> >> > TCGA methylation data is background corrected and dye bias equalized >> > (for >> > the 450k samples, at least, and as b ...
written 7.1 years ago by Brent Pedersen90
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Comment: C: Question about interpretation of CHARM results
... On Sun, Aug 19, 2012 at 2:21 PM, Tim Triche, Jr. wrote: > (a bit late, but better late than never) > > Dr. Coombes is right, of course, and I ought to have mentioned this > earlier. It is a thorny issue, especially with epidemiological studies. > Cancer, less so. > > For diff ...
written 7.1 years ago by Brent Pedersen90
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Answer: A: batch effects 450K
... On Fri, Jun 8, 2012 at 8:44 AM, Femke [guest] wrote: > > Dear All, > > I have Infinium 450K data for 56 breast cancer tumors. As a first analysis I wanted to do a clustering and see the distribution of the samples. For this I used the minfi package. Unfortunately, the assays were done i ...
written 7.3 years ago by Brent Pedersen90

Latest awards to Brent Pedersen

Popular Question 4.8 years ago, created a question with more than 1,000 views. For Gviz DataTrack, type="densityplot"
Popular Question 4.8 years ago, created a question with more than 1,000 views. For sva::ComBat without covariate of interest?

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