User: Shian Su

gravatar for Shian Su
Shian Su20
Reputation:
20
Status:
New User
Location:
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Last seen:
2 months ago
Joined:
3 years, 7 months ago
Email:
s***@wehi.edu.au

Posts by Shian Su

<prev • 12 results • page 1 of 2 • next >
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Comment: C: What to do when a bug is found in a BioConductor package (Glimma)
... 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 8 weeks ago by Shian Su20
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Answer: A: Why does the Glimma package require R >= 3.4.0 ?
... 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 19 months ago by Shian Su20
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Comment: C: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... 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 23 months ago by Shian Su20
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Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
...   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" ...
annotationdbi homo.sapiens written 23 months ago by Shian Su20 • updated 23 months ago by Johannes Rainer1.5k
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Comment: C: Cannot create SingleCellExperiment object
... 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 23 months ago by Shian Su20
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Cannot create SingleCellExperiment object
...   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 <- ...
singlecellexperiment written 23 months ago by Shian Su20 • updated 23 months ago by Aaron Lun25k
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Comment: C: How do you test a contrast in MAST?
... 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 2.1 years ago by Shian Su20
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How do you test a contrast in MAST?
... 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 ...
differential gene expression single-cell mast written 2.1 years ago by Shian Su20 • updated 2.1 years ago by Andrew_McDavid190
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Comment: C: Does Rhtslib currently work on Windows?
... 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 2.2 years ago by Shian Su20
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Comment: C: Does Rhtslib currently work on Windows?
... 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. ...
written 2.2 years ago by Shian Su20

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