User: Dave Tang

gravatar for Dave Tang
Dave Tang210
Reputation:
210
Status:
Trusted
Location:
Australia/Perth/UWA
Website:
https://davetang.org/muse
Twitter:
davetang31
Scholar ID:
Google Scholar Page
Last seen:
4 months ago
Joined:
7 years, 5 months ago
Email:
d***************@gmail.com

Computational biologist.

Posts by Dave Tang

<prev • 22 results • page 1 of 3 • next >
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Downstream analysis after using mnnCorrect()
... Hello, I have several batches of scRNA-seq data, which are biological replicates, and would like to use mnnCorrect() from the scran package to correct for batch effects. Each batch should have a quite a different cell type composition, which is why I would like to use the MNN method. From the help ...
scran mnncorrect written 8 months ago by Dave Tang210 • updated 8 months ago by Aaron Lun21k
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Parsing error with getVariants() from the myvariant package
... Hello, I'm trying to use the myvariant package but I'm getting a parsing error. Here's an example: library(VariantAnnotation) library(myvariant) file.path <- system.file("extdata", "dbsnp_mini.vcf", package="myvariant") vcf <- readVcf(file.path, genome="hg19") hgvs <- formatHgvs(vcf, va ...
myvariant written 20 months ago by Dave Tang210 • updated 20 months ago by cyrus.afrasiabi20
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Comment: C: RefSeq coordinates from biomaRt
... On Mon, 25 Nov 2013 22:04:23 +0900, Sean Davis wrote: > You'll want to use "transcript_start" and "transcript_end" rather than > "start_position" and "end_position". Thank you so much Sean! I spent the entire afternoon looking in all the wrong places. Cheers, -- Dave ...
written 4.9 years ago by Dave Tang210
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Comment: C: RefSeq coordinates from biomaRt
... On Mon, 25 Nov 2013 19:31:22 +0900, Sean Davis wrote: > Hi, Dave. > > There may be multiple issues going on here, so you'll have to do some > digging yourself when discrepancies arise like you see here. Working > through your first example, keep in mind that neither Ensembl or UCSC ...
written 4.9 years ago by Dave Tang210
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RefSeq coordinates from biomaRt
... Hello, I've been using biomaRt to fetch genomic coordinates of RefSeqs (perhaps in an incorrect manner?). I found that the RefSeq coordinates don't match the coordinates provided at the UCSC Genome Browser (NM_033453 at chr20:3190006-3204516): library("biomaRt") ensembl <- useMart("ensembl", da ...
biomart written 4.9 years ago by Dave Tang210 • updated 4.9 years ago by Sean Davis21k
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Comment: C: Unable to find an inherited method for function ‘exprs’
... On Wed, 14 Aug 2013 13:48:42 +0900, Wolfgang Huber wrote: > I think many people have experienced that taking code examples that one > saw somewhere and trying to tweak them to one's own problem by trial and > error can be an efficient way to move forward; however, when it fails, > it i ...
written 5.2 years ago by Dave Tang210
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Comment: C: Unable to find an inherited method for function ‘exprs’
... On Wed, 14 Aug 2013 12:13:31 +0900, Wolfgang Huber wrote: > Dear Dave > this is actually not an error. The function 'exprs' expects and > argument, and since you are giving it none, it complains, and one should > not blame it for that. > Perhaps can you tell us what you want to achi ...
written 5.2 years ago by Dave Tang210
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Unable to find an inherited method for function ‘exprs’
... Hello, I'm getting this error when trying to use the exprs() function from the Biobase package: library(Biobase) exprs() Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?exprs? for signature ?"missing"? I was trying to use the virtualArray package, ...
biobase geoquery virtualarray written 5.2 years ago by Dave Tang210 • updated 5.2 years ago by Wolfgang Huber13k
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Comment: C: GEOquery getGEO error in read.table
... On Wed, 09 Jan 2013 06:39:52 +0900, Dan Tenenbaum wrote: > Several BioC packages that download data from GEO failed to build last > night, in a way that suggests GEO was at least partially down last > night. > I could reproduce the error earlier today but it works now. Dear Sean, Dan ...
written 5.8 years ago by Dave Tang210
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GEOquery getGEO error in read.table
... Dear mailing list, I've been trying to use GEOquery to fetch microarray data from GEO but to no avail. I've searched online and found several discussions about a similar problem but the bug was solved for an older version. Here I've just tried to run the first couple of steps of the vignette: lib ...
microarray geoquery written 5.8 years ago by Dave Tang210 • updated 5.8 years ago by TEXTORIS Julien160

Latest awards to Dave Tang

Popular Question 4 months ago, created a question with more than 1,000 views. For GEOquery getGEO error in read.table
Popular Question 19 months ago, created a question with more than 1,000 views. For Unable to find an inherited method for function ‘exprs’
Epic Question 19 months ago, created a question with more than 10,000 views. For Unable to find an inherited method for function ‘exprs’
Popular Question 19 months ago, created a question with more than 1,000 views. For RefSeq coordinates from biomaRt
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Unable to find an inherited method for function ‘exprs’
Great Question 4.1 years ago, created a question with more than 5,000 views. For Unable to find an inherited method for function ‘exprs’

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