## User: snf

snf0
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4 years, 5 months ago
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#### Posts by snf

<prev • 5 results • page 1 of 1 • next >
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... I was having the same issue, but it seems to be solved by upgrading to bioconductor 3.2, which installs ggbio v 1.18.3 among other things. I was at 3.1 beforehand. Still receive this warning: "gap" not in any of the valid gene feature terms "cds", "exon", "utr" but a plot is generated. Hope that ...
written 3.2 years ago by snf0
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... Hello -  I was going through the RNASeqGene workflow today (http://www.bioconductor.org/help/workflows/rnaseqGene/) and I think there may be a minor typo inside. When creating the first summarizedExperiment the workflow says "This experiment was not strand-specific so we set ignore.strand to FALSE. ...
written 4.2 years ago by snf0
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... The immediate downstream use is for clustering by row, where each column of the row represents a different biological state.  I have strong reason to believe that there is large variability between some of these samples (e.g. some are cytoplasmic and some nuclear), so based on the ?rlog page "If man ...
written 4.5 years ago by snf0
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... Thanks Wolfgang. I did try to perform the rlog transform after collapsing reps, but received an error: ddsCollapsed <- collapseReplicates(dds, groupby=dds$fraction, run=dds$Run) avgrld <- rlog(ddsCollapsed, blind=FALSE) Error in estimateDispersionsGeneEst(object, quiet = TRUE) : the num ...
written 4.5 years ago by snf0
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