User: linda.c.dansereau

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Posts by linda.c.dansereau

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Comment: C: How does newSCESet calculate expression matrix
... Thanks for the link! I completely agree there are better ways to have designed this, but alas, circumstances didn't make it possible. I didn't do any of the data collection, just playing with the results to understand how these analyses work, and build up skills. Used it because of circumstances but ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... Thank you for the insight and suggestions. I'll give those a try. Just to explain the data a bit. The RNA was collected ages ago from patched C. elegans neurons for a different purpose and then ended up sitting in the freezer for a few years. The RNA-seq data was obtained a couple years ago I think ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... Below are my plots from the old (top) and new (bottom) versions with the trendline in blue. The HVGs (yellow) in the first graph are at an FDR of 0.05 and in the second graph at an FDR of 0.5. Top graph code: sce_1 <- computeSpikeFactors(sce_1, general.use=TRUE) sce_1 <- normalize(sce_1) v ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... Ah thanks. I switched when I was trying to get the 1.4.0 version initially and forgot to switch back. :)   As far as I can tell the trend line is the first major difference between my analysis with the earlier version and the newest version of scater. As I'm a relative newbie in troubleshooting R c ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... I don't seem to be able to specify the trend method anymore. When I do I get an error message about an unused argument.  var.fit.2 <- trendVar(sce_2, trend="loess", use.spikes=FALSE, span=0.3) Error in .trend_var(mat, ..., subset.row = subset.row) :    unused argument (trend = "loess") Would th ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... Thanks for the reply. I haven't had a chance to take a closer look at the changes in the last couple weeks. The most obvious effect is when I used trendVar and decomposeVar to identify highly variable genes the number of hvg's with an FDR <= 0.05 went from 807 to 0 in one case and 13 to 2 in anot ...
written 3 months ago by linda.c.dansereau0
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Comment: C: How does newSCESet calculate expression matrix
... On a slightly related note I noticed a dramatic change in my results using scater when I recently updated R from version 3.3.2 to version 3.4.1, leading to the update from scater_1.2.0 to scater_1.3.35. Could this be due to the change in how you calculate exprs?  If using scater_1.4.0 makes a diffe ...
written 4 months ago by linda.c.dansereau0
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Comment: C: How to process ids containing "." in BiomaRt?
... Ah, thanks for finding that. ...
written 4 months ago by linda.c.dansereau0
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How to process ids containing "." in BiomaRt?
... Hello, I am trying to annotate an SCEset using getBMFeatureAnnos where the filter column contains values such as "MTCE.31" and "MTCE.23". In making the SCEset these are recognized as different row names, however when running the getBM function the ".31" and ".23" are ignored and they are interprete ...
annotation biomart sce written 4 months ago by linda.c.dansereau0 • updated 4 months ago by Mike Smith2.1k

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