User: Andrew Jaffe

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Andrew Jaffe120
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Posts by Andrew Jaffe

<prev • 12 results • page 1 of 2 • next >
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Gviz - Visualize Reads - Color by Presence of Junction?
... Hey, I started playing around with Gviz for visualizing aligned RNAseq reads and have been pretty impressed, particularly with integrating external annotation with read-level data. I've been able to get multi-paneled plots depicting reads and corresponding coverage in specific regions - I wanted t ...
coverage gviz written 5.8 years ago by Andrew Jaffe120 • updated 5.8 years ago by Robert Ivanek640
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TxDb.Hsapiens.UCSC.hg19.knownGene: seqlevels() vs isActive()
... Was there a new version of TxDb.Hsapiens.UCSC.hg19.knownGene in the last day or two (v 2.9.2)? It looks like there are some issues with seqlevels replacing isActiveSeq() in the new version: > library(TxDb.Hsapiens.UCSC.hg19.knownGene) > txdb=TxDb.Hsapiens.UCSC.hg19.knownGene For example, I n ...
written 6.1 years ago by Andrew Jaffe120 • updated 6.1 years ago by Marc Carlson7.2k
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saving GRanges objects - resulting file size issue
... Hey, I'm trying to save several GRanges objects in the same rda file, but for some reason, one of the smaller GRanges objects (~23Mb) makes the saved file go from 25Mb to 9Gb+ and I'm unsure of why exactly, and have never seen this problem before: > class(exons) [1] "GRanges" attr(,"package") [ ...
go written 6.1 years ago by Andrew Jaffe120 • updated 6.1 years ago by Valerie Obenchain6.7k
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Answer: A: CHARM - The following columns in sampleKey...
... Hey, What's actual code you are running? It looks like you read the data in with readCharm: rawData = readCharm(...) So is that discrepancy just a warning, and not an error? Also, if you are using a methyl-enrichment protocol (like MeDip) with the charm package, you need to reverse the inputs - ...
written 6.9 years ago by Andrew Jaffe120
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Question about interpretation of CHARM results
... > What about peripheral blood where one may be measuring a signal from a variety of cell types or tissues? This would probably prove useful to you - I've played around with it, and ~450 of their training set probes are on the 450k. You can email the authors for their code. http://www.biomedcentr ...
written 7.1 years ago by Andrew Jaffe120
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Answer: A: Question about interpretation of CHARM results
... I'm jumping in here kind of late, but hopefully can help you out. The first thing, like Brian suggested, is to make sure the inputs are reversed (because the Charm data has unmethylated as the "enriched" sample), as you're using MeDip data. However, since you are actually getting log- ratio differen ...
written 7.1 years ago by Andrew Jaffe120
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Back-estimating batch variables from SVA for ComBat?
... Hollis, There's no need to "estimate" the batch inputs for ComBat after running SVA - you can just adjust for the surrogate variables themselves in any downstream analyses. For something like WGCNA, or any other clustering algorithm, you can regress the surrogate variables out of the expression dat ...
sva written 7.1 years ago by Andrew Jaffe120 • updated 7.1 years ago by wrighth260
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Comment: C: GOstats - internal filtering?
... > The only GO terms that are tested are those that arise from mapping your Entrez Gene IDs to GO terms. Just to be clear, you mean by mapping the *significant*/selected Entrez Gene IDs (say by a differential expression analysis) to GO terms? Because the universe/possible Entrez Gene IDs on the mi ...
written 7.4 years ago by Andrew Jaffe120
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GOstats - internal filtering?
... Hopefully I can get a quick answer to this question about GOstats. I'm trying to calculate enrichment for every GO category using the GOstats package. I would assume that setting the p-value cutoff = 1 with conditional=FALSE would give me an enrichment odds ratio/p-value for every GO category in, s ...
annotation go hgu133plus2 gostats category written 7.4 years ago by Andrew Jaffe120 • updated 7.4 years ago by James W. MacDonald51k
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Answer: A: batch effect confounded with condition
... We clearly need more information about your experiment to help you with removing batch effects. Judging from your original email, it sounded like all of condition 1 was on batch 1 and all of condition 2 was run on batch 2 (ie this is perfect confounding). What exactly was run on Batch 1 (experiment ...
written 7.5 years ago by Andrew Jaffe120

Latest awards to Andrew Jaffe

Popular Question 5.8 years ago, created a question with more than 1,000 views. For Back-estimating batch variables from SVA for ComBat?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For rtracklayer::liftOver ordering
Popular Question 5.8 years ago, created a question with more than 1,000 views. For saving GRanges objects - resulting file size issue
Popular Question 5.8 years ago, created a question with more than 1,000 views. For TxDb.Hsapiens.UCSC.hg19.knownGene: seqlevels() vs isActive()
Popular Question 5.8 years ago, created a question with more than 1,000 views. For saving GRanges objects - resulting file size issue

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