User: VSM

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VSM120
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120
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Location:
United Kingdom
Last seen:
3 months, 1 week ago
Joined:
5 years, 1 month ago
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v**************@igmm.ed.ac.uk

Posts by VSM

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Comment: C: processing of (salmon) gene counts for eqtl analysis
... Michael, that is super helpful. Thank you!! ...
written 3 months ago by VSM120
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Comment: C: processing of (salmon) gene counts for eqtl analysis
... Thanks Michael. I still have a few issues ... 1. If I re-import with DESeqDataSetFromTximport, can I supply TMM normalisation factors to your code snippet? (I know they are similar but I guess not identical (?), and I want to stay consistent with previous analyses I run). I don't know what (if any) ...
written 3 months ago by VSM120 • updated 3 months ago by Michael Love19k
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processing of (salmon) gene counts for eqtl analysis
... Hi there I have a question about the appropriate salmon-generated gene counts, which take into account gene length, for the purpose of running eqtl analysis. I would much appreciate your suggestions on this. I used tximport to obtain gene-level counts/abundance estimates for our RNAseq data (estim ...
tmm salmon gene length tximport eqtl written 3 months ago by VSM120 • updated 3 months ago by Michael Love19k
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Comment: C: illuminaHumanv4.db : annotation source, and mapping to transcript names
... Hi James,  Thank you for the tips, I thought that might be too time consuming, but your suggestions should get me there faster! ...
written 2.8 years ago by VSM120
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Comment: C: illuminaHumanv4.db : annotation source, and mapping to transcript names
... Hi James,  Yes, that is where I obtained the information in my original post (point 1) above. I hadn't noticed the ENSEMBL only annotation (mentioned by Efstathios), which clarifies my assumption.  I still cannot find transcript ids for the re-annotated piepline (EnsemblReannotated, etc), though. ...
written 2.8 years ago by VSM120
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Comment: C: illuminaHumanv4.db : annotation source, and mapping to transcript names
... Hi Efstathios There are various HT12 re-annotations that are getting published all the time, so the challenge is to find one that is most reliable. For the illuminaHumanv4.db package, I am trying to identify what this reannotation is, and how it differs to something like standard ensembl. I am uncl ...
written 2.8 years ago by VSM120
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Comment: C: illuminaHumanv4.db : annotation source, and mapping to transcript names
... Thanks Efstathios,  I didn't notice that, I mostly looked at the documentation. Would you happen to know what the difference between ENSEMBL and EnsemblReannotated ( illuminaHumanv4ENSEMBLREANNOTATED) is? I would assume that the former is actually directly derived from the ensembl annotation, whil ...
written 2.8 years ago by VSM120
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illuminaHumanv4.db : annotation source, and mapping to transcript names
... Hi there I have been using the R package illuminaHumanv4.db to annotate our HT12 v4 array probes, and I have two questions: * The description of the package says the data is assembled from public repositories. However, the reference manual notes that extensive reannotation has been carried out for ...
microarray annotation illumina human ht-12 v4 written 2.8 years ago by VSM120
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Excluding probes during methylation analysis
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 4.8 years ago by VSM120
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Comment: C: Excluding probes during methylation analysis
... The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. ...
written 5.1 years ago by VSM120

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