## User: Shian Su

Shian Su20
Reputation:
20
Status:
New User
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Last seen:
4 days, 15 hours ago
Joined:
3 years, 5 months ago
Email:
s***@wehi.edu.au

#### Posts by Shian Su

<prev • 12 results • page 1 of 2 • next >
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... Thanks for the bug report Samuel. As Gordon mentioned, I would prefer bugs be submitted through Github issues. The reason for the bug is that I've rounded all values to 4 significant places to avoid values with tens of digits, it's clear that this causes confusion for large numeric values so I'll up ...
written 4 days ago by Shian Su20
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... It doesn’t use any features from the latest R release, however it is Bioconductor policy to use require the latest R version on all packages. If you know how to change the dependency in the DESCRIPTION file then the package will work perfectly fine on an older version of R. ...
written 17 months ago by Shian Su20
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... Thanks Johannes, that's very helpful. Do you know if there are any major differences between the AH##### databases and Homo.sapiens that I should be aware of? ...
written 21 months ago by Shian Su20
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...   I'm trying to use Homo.sapiens to annotate genes from my count matrix. However I never seem to find any genes from chrM. library(Homo.sapiens) all_genes <- biomaRt::select( Homo.sapiens, key = keys(Homo.sapiens, keytype = "GENEID"), keytype = "GENEID", columns = c("CDSCHROM" ...
written 21 months ago by Shian Su20 • updated 21 months ago by Johannes Rainer1.5k
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... Thanks Aaron, following that other question thread lead me to the solution. I had been drawing most of the BioC packages from a shared location I have no access to. The solution was to use biocLite("SingleCellExperiment", dependencies=TRUE, lib="~/R/library") to get a copy of all the dependencies ...
written 22 months ago by Shian Su20
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...   Using R 3.4.2, BioC 3.6, SingleCellExperiment_1.0.0. The following example code from ?SingleCellExperiment produces an error   library(SingleCellExperiment) ncells <- 100 u <- matrix(rpois(20000, 5), ncol=ncells) v <- log2(u + 1) pca <- matrix(runif(ncells*5), ncells) tsne <- ...
written 22 months ago by Shian Su20 • updated 22 months ago by Aaron Lun24k
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... Thanks, I guess having an intercept model is fine. Is this interface for contrasts documented anywhere? I couldn't quite work it out from the vignette and help pages. ...
written 23 months ago by Shian Su20
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... I am trying to analyse some single cell RNA seq data with MAST, currently I'm using an edgeR pipeline and I cannot work out how to properly test a contrast in MAST. The experimental setup is a 3x2 with 3 strains and 2 conditions, I'd like to test differential expression between the conditions withi ...
written 23 months ago by Shian Su20 • updated 23 months ago by Andrew_McDavid190
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... Thanks so much Martin, the necessary code was to add import(Rhtslib) to the NAMESPACE, which I did via ROxygen's @import for consistency.  I still needed the zlibbioc::pkgconfig() code because I actually reference zlib directly in some of my c++. I'll post these to the dev mailing list in ...
written 2.0 years ago by Shian Su20
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... Yes that zlibVersion was a typo, wasn't logged into bioconductor on my Windows testing laptop so I typed out the error message. Thanks for the help, I'll try it out once I'm infant of a Windows laptop again. ...