User: Aaron Mackey

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Aaron Mackey160
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Posts by Aaron Mackey

<prev • 16 results • page 1 of 2 • next >
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Answer: A: enabling reproducible research & R package management & install.package.version
... On Mon, Mar 4, 2013 at 4:13 PM, Cook, Malcolm wrote: > * where do the dragons lurk > webs of interconnected dynamically loaded libraries, identical versions of R compiled with different BLAS/LAPACK options, etc. Go with the VM if you really, truly, want this level of exact reproducibility. ...
written 6.3 years ago by Aaron Mackey160
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how to supply a vector/list of results to GenTable in topGO?
... The GenTable() function in topGO expects an explicitly enumerated set of result objects as parameters; but I've got them in a list, and don't want to hard-code the names/results. Is there a way to dynamically build the parameters as a string and have the string evaluated as such when calling GenTab ...
topgo written 6.4 years ago by Aaron Mackey160
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Comment: C: Is there any prejudice whether to use edgeR or DESeq for differential expression
... RSEM counts are indeed counts (not a normalized/scaled FPKM), but for the relatively small subset of reads that are ambiguously mapped ("multi-mapped"), then the count for that read gets broken up across the (probabilistically-weighted) possibilities. So the final counts are non-integer. We (and o ...
written 6.6 years ago by Aaron Mackey160
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Comment: C: normalizing RNAseq with batch/block-level bulk DE
... I meant that the experimental design contains both factors of interest, and nuisance factors, both of which contribute to variation across samples. While the factors of interest may relate to a small number of gene/isoform changes (with potentially large magnitudes), the nuisance factor differences ...
written 6.7 years ago by Aaron Mackey160
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normalizing RNAseq with batch/block-level bulk DE
... Is VST-normalization (a la DESeq) considered the right way to deal with large scale differences in mean "baseline" expression across experimental blocks? Is there a normalization method that can take into account the design matrix (or at least the batch/block columns)? I don't want to remove the b ...
normalization edger written 6.7 years ago by Aaron Mackey160 • updated 6.7 years ago by Wolfgang Huber13k
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Comment: C: A metric to determine best filtration in the limma package
... As Gordon Smyth and others have commented on, such FPKM normalization is not necessary/useful if differential expression across treatments is the goal. Yes, this particular filter will have some bias against smaller transcripts who naturally have fewer total counts, but one major intent of the filt ...
written 6.8 years ago by Aaron Mackey160
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Comment: C: RNA-seq data simulation
... Try FluxSimulator, or BEERS, both mentioned in this thread: http://seqanswers.com/forums/showthread.php?t=5386 -Aaron On Tue, Aug 21, 2012 at 11:00 AM, Mark Robinson wrote: > > You could start with rnbinom(). The 'size' argument is 1/dispersion. > > Mark > > On 21.08.2012, a ...
written 6.8 years ago by Aaron Mackey160
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Comment: C: Using limma for quantitative proteomics data
... There's a thread on the bioconductor mailing list about using voom for RSEM-based RNA-seq quantification, in which Gordon Smythe explained that while voom() was designed for count data, it doesn't require it. As Tim Triche has suggested, if you're raw data is really ratios (and not absolute values ...
written 7.0 years ago by Aaron Mackey160
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Answer: A: Using limma for quantitative proteomics data
... yes, it should be possible with a voom()-based analysis to get the variances "right". -Aaron On Tue, Jun 19, 2012 at 12:47 PM, Yong Li wrote: > Hello, > > limma has been so valuable in microarray data analysis, but has anyone > used limma for finding differentially expressed proteins ...
written 7.0 years ago by Aaron Mackey160
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Answer: A: LIMMA: plotMDS
... All genes contribute to all principle components; some just more than others. I've found it useful (or perhaps just entertaining) to see heatmaps of the first N (say 10) component loadings, constrained to the 500 genes whose variances contribute most to those components. -Aaron On Sun, May 6, 201 ...
written 7.1 years ago by Aaron Mackey160

Latest awards to Aaron Mackey

Popular Question 6.3 years ago, created a question with more than 1,000 views. For convert between MethylLumiSet (methylumi) and RGChannelSet (minfi)

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