User: davis

gravatar for davis
davis90
Reputation:
90
Status:
Trusted
Location:
United Kingdom
Twitter:
@davisjmcc
Last seen:
1 year, 7 months ago
Joined:
3 years, 10 months ago
Email:
d****@ebi.ac.uk

NHMRC Early Career Fellow

Stegle Group

European Bioinformatics Institute (EMBL-EBI)

Hinxton, Cambridgeshire

Posts by davis

<prev • 11 results • page 1 of 2 • next >
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Answer: A: is SCEset fully abandoned in scran?
... Yes, that is correct. Both scater and scran are completely switching to SingleCellExperiment for the next Bioconductor release. The functions “toSingleCellExperiment()” and “updateSCESet()” in scater will convert an existing SCESet object to a SingleCellExperiment object for you. — Davis McCarthy ...
written 21 months ago by davis90
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Answer: A: problems when working with SingleCellExperiment object in scater
... Thanks for the bug report! I've just commited (to Bioc devel) fixes for the `colSums` issues and adjusted `read10xResults` so that it coerces 10x data to a `dgCMatrix` automatically. We're still working through all of the other possibilities and adding tests, so the `rowVars` issue you experienced ...
written 22 months ago by davis90
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Comment: C: How does newSCESet calculate expression matrix
... That’s a reminder to update the vignette…which is on the to-do list. Davis — Davis McCarthy NHMRC Early Career Fellow Stegle Group EMBL-EBI, Cambridge, UK www.ebi.ac.uk > On Thursday, May 25, 2017 at 5:26 pm, Aaron Lun [bioc] <noreply@bioconductor.org mailto:noreply@bioconductor.org)=""> ...
written 2.2 years ago by davis90
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Answer: A: How does newSCESet calculate expression matrix
... OK, you haven’t told us what version of scater you’re using, so I’ll assume it’s the latest version, 1.4.0. From the documentation for newSCESet (Details section): “...an SCESet object will contain exprs values; these will be computed as log2(*pm + offset) values if a data type higher in the hierar ...
written 2.2 years ago by davis90
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Comment: C: How did the edgeR authors compute Figure 2 (genewise deviance statistics?)
... I had forgotten about the gof() function! :) ...
written 2.3 years ago by davis90
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Answer: A: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
... Hi Gabriel I'm not sure that I can describe this more concisely than in the original figure caption: "QQ-plots of goodness of fit statistics using common, trended or empirical Bayes genewise (tagwise) dispersions. Genewise deviance statistics were transformed to normality, and plotted against theor ...
written 2.3 years ago by davis90 • updated 2.3 years ago by Gordon Smyth38k
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Answer: A: using SC3 and scater for bulk-RNAseq
... Hi Assa It is certainly possible and makes sense to use scater for bulk RNA-seq data. I expect that SC3 would also work well on bulk RNA-seq data. The authors of that package could offer more insight, but a priori I think it would perform well in this setting as well. Normalised values (if they ...
written 2.4 years ago by davis90
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Bug in rhdf5::h5write?
... I think I might have found a bug in rhdf5. Namely, calling the following in a session where library(rhdf5) has *not* been run: `rhdf5::h5write(donors, file = output_file, name = "sampleID")` (where "donors" is a character vector) gives the following error: ``` Error in UseMethod("h5write") :   no ap ...
rhdf5 written 2.5 years ago by davis90 • updated 2.5 years ago by Mike Smith3.8k
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Comment: C: searching for edgeR version 2.2.6
... I absolutely agree with Aaron. Bioconductor 2.8 was released in April 2011, so by using edgeR v2.2.6 you're missing out on almost 6 years of methodological improvements and bug fixes. I *can* remember a time when glmLRT accepted those arguments, but nevertheless strongly advise you to update you ...
written 2.5 years ago by davis90
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Answer: A: Should edgeR-GLM on single cell RNA data be performed on the counts or normalize
... You should use the counts with edgeR. scran computes size-factors for normalization comparable to those from TMM, but with some smart adjustments to appropriately compute size factors from scRNA-seq data with lots of dropouts. As such, size factors from scran are used in an edgeR workflow in the sa ...
written 3.0 years ago by davis90

Latest awards to davis

Scholar 2.3 years ago, created an answer that has been accepted. For A: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
Scholar 2.3 years ago, created an answer that has been accepted. For A: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Question: How did the edgeR authors compute Figure 2 (genewise deviance statisti
Autobiographer 3.3 years ago, has more than 80 characters in the information field of the user's profile.

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