User: snf

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snf0
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Posts by snf

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Cannot get ggbio autoplot to run successfully on R 3.2 (3.2.2 or 3.2.3)
... 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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Minor error in the RNASeqGene workflow
... 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. ...
rnaseqgene written 4.2 years ago by snf0
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Answer: A: DESeq2: combine replicates following rlog transformation for visualization, clus
... 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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Answer: A: DESeq2: combine replicates following rlog transformation for visualization, clus
... 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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DESeq2: combine replicates following rlog transformation for visualization, clustering
... Hello -  I have a series of 12 seq datasets with two replicates and would like to perform clustering analysis of the rlog-normalized data. However, after rlog transformation, I still have two replicates for each dataset and therefore have to combine the reps in some way before clustering.  I have t ...
rnaseq deseq2 written 4.5 years ago by snf0

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