User: David Eccles (gringer)

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New Zealand
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Posts by David Eccles (gringer)

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Comment: C: Combining multiple L2FC values and determining variance
... Your (1) is what I'm trying to do here. Getting the average L2FC is easy, I just don't know how to properly estimate the error. I'll pair this up with a visualisation of the normalised *expression* values. Again, that's an easy bit - the values are single data points (rather than relative values), ...
written 11 weeks ago by David Eccles (gringer)10
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Combining multiple L2FC values and determining variance
... How do I calculate the error associated with aggregated L2FC values? I'd like to combine multiple differential expression values into a single statistic, with variance, to express how genes in the mitochondrial complexes change (or don't change) compared to wildtype cell lines under certain conditi ...
deseq2 written 11 weeks ago by David Eccles (gringer)10
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Comment: C: Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a t
... Thanks for that insight. I used vst for my last differential expression analysis, and really liked it (especially after length-based scaling, which I called *vstpk*). I thought that rlog was a newer, better approach. I think you've given me the little nudge I needed to revisit vst again. ...
written 4 months ago by David Eccles (gringer)10
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Comment: C: Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a t
... Read orientation *is* necessary for the discoveries we're carrying out. The most relevant for us is negative strand expression on the mitochondrial genome in unannotated regions. I appreciate that this is mostly not going to be picked up by mapping to a transcriptome, and am on the lookout for alte ...
written 4 months ago by David Eccles (gringer)10
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Comment: C: Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a t
... Thanks. I understand that in addition to the A-tail anchoring there are isoform annotation issues which mean that there might be incorrect assignment. Would you recommend preprocessing using something like tximport to convert the transcript counts to gene counts? On second thoughts, I notice that t ...
written 4 months ago by David Eccles (gringer)10
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Is it appropriate to use DESeq2 to analyse MinION data that's been mapped to a transcriptome?
... More generally, how should we calculate differential expression of genes (or transcripts) based on long-read nanopore data? Is there some option I can activate to get our long reads to work better with DESeq2 (or any other tool)? My core problem is that the Log2FC values reported by DESeq2 do not ...
deseq2 nanopore written 4 months ago by David Eccles (gringer)10
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Comment: C: DESeq2 -- Comparing factors while fixing another factor
... Thanks Mike. We're very aware that the DESeq2 version is out of date, but need to keep to the older version for reproducibility purposes -- there's already been a whole lot of downstream analysis and validation based on 1.6.3 results from a previous run. I'll make sure that our software is all upgr ...
written 3.8 years ago by David Eccles (gringer)10
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DESeq2 -- Comparing factors while fixing another factor
... I want to know the most appropriate way to compare one group within another group when doing a differential expression test. In our analysis, we have two cell populations (CD11b, TN) and two treatment conditions (UT, DBP.FITC). I want to know how I should compare different treatments within a cell ...
deseq2 differential gene expression multiple factor design written 3.8 years ago by David Eccles (gringer)10 • updated 3.8 years ago by Michael Love25k
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h5ls spits out errors when iterating ONT Fast5 files
... h5ls has traversal errors when traversing an HD5 structure created from the MinION. The errors don't seem to cause problems with the output, but there's no way to hide them: > library(rhdf5); > fast5.files <- list.files(pattern="\\.fast5"); > fastFile <- fast5.files[1]; > fastH5F ...
rhdf5 written 4.0 years ago by David Eccles (gringer)10 • updated 4.0 years ago by Bernd Fischer540
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DESeq2 -- Bootstrap subsampling to estimate distribution of expression
... I'm working in collaboration with a clinical diagnostics / research team in New Zealand, trying to use RNA biomarkers to determine disease risk. What we would ideally like to do is to generate expression ranges (in log space) using the reference samples, and then use those ranges to generate individ ...
deseq2 differential expression bootstrap written 4.5 years ago by David Eccles (gringer)10 • updated 4.5 years ago by Michael Love25k

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Popular Question 3.8 years ago, created a question with more than 1,000 views. For DESeq2 -- Comparing factors while fixing another factor

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