User: poecile.pal

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Posts by poecile.pal

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Comment: C: DRIMSeq with technical replicates
... Oh, I read about the disadvantages of cross-posting, I think I'll delete the post from here. ...
written 9 weeks ago by poecile.pal0
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Comment: C: DRIMSeq with technical replicates
... Hello Kevin, Yes, thanks, I have duplicated this post on another forum just in case. Best regards, Poecile palustris ...
written 9 weeks ago by poecile.pal0
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DRIMSeq with more than 2 categories in the group
... Good evening, I'd like to perform a DRIMSeq analysis with more than 2 categories in the group. Later I considered two categories (control and sick): n.small<-min(table(DRIMSeq::samples(d)$condition)) #How many samples are in the smallest group n.big<-max(table(DRIMSeq::samples(d)$co ...
software error R rna-seq written 4 months ago by poecile.pal0
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Error in alpha * 100 : non-numeric argument to binary operator (problem with stageR)
... Hello all, I am trying to repeat actions from the tutorial http://bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html#statistical-analysis-of-differential-transcript-usage. My actions were: library(DEXSeq) sample.data_kaskad <- DRIMSeq::samples(d_kas ...
software error R rna-seq sequencing written 6 months ago by poecile.pal0
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Comment: C: How to create tx2gene object with gene names from annotation
... Thank you a lot, I have never heard about this package. ...
written 7 months ago by poecile.pal0
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How to create tx2gene object with gene names from annotation
... Hello all, I would like to have `tx2gene` object with 3 columns - the third column should be with gene names like PLA2G4A etc. The using annotation looks like this: ##description: evidence-based annotation of the human genome (GRCh38), version 32 (Ensembl 98) ##provider: GENCODE ##con ...
software error R rna-seq written 7 months ago by poecile.pal0 • updated 7 months ago by Papyrus370
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Comment: C: DRIMSeq problems with dmPrecision
... Thank you a lot, I tried to repeat with the `d3` with 34% of the initial number of genes (it was obtained after the strong filtering), and with d2 (25%), but had the same problem( Possibly, should I filter more and more strictly? I think, leaving 34% and 25% - it's very strict? > d <- dm ...
written 7 months ago by poecile.pal0
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DRIMSeq problems with dmPrecision
... Hello all, I would like to use DRIMSeq (tutorial - https://bioconductor.org/packages/release/bioc/vignettes/DRIMSeq/inst/doc/DRIMSeq.pdf) In one moment I performed step dmPrecision: > d <- dmPrecision(d, design = design_full) ! Using a subset of 0.1 genes to estimate common precision ...
software error R rna-seq sequencing written 7 months ago by poecile.pal0 • updated 7 months ago by kristoffer.vittingseerup3.4k

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