User: d-joester

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d-joester20
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7 months, 3 weeks ago
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d********@northwestern.edu

Posts by d-joester

<prev • 6 results • page 1 of 1 • next >
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Answer: A: stageR: Error in stageWiseAdjustment
... See answer in comment. "Add Answer" text entry is broken. ...
written 7 months ago by d-joester20
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Comment: C: stageR: Error in stageWiseAdjustment
... It turns out I should have paid more attention to the following: > Because of how the stageR package will combine transcript and gene > names, we need to strip the gene and transcript version numbers from > their Ensembl IDs (this is done by keeping only the first 15 > characters of the ...
written 7 months ago by d-joester20
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stageR: Error in stageWiseAdjustment
... Hi, I am very new to RNAseq, bioconductor, and R. So far, I have successfully established my workflow for DGE of my data. I used Salmon to generate an index against the reference [transcriptome][1] of the purple sea urchin, *S. purpuratus*. I further used Salmon to create transcript-level count tab ...
dexseq drimseq stager rnaseqdtu written 7 months ago by d-joester20
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Answer: A: tximport: Error in medianLengthOverIsoform
... Poking around, I found that setdiff(rownames(cts),tx2gene$TXNAME) revealed that tx2gene was missing three transcripts. I added these to my csv file and the issue disappeared. ...
written 7 months ago by d-joester20
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Comment: C: tximport: Error in medianLengthOverIsoform
... Michael, thanks for your quick response. I used Salmon to create an index of the reference transcriptome for *S. purpuratus* hosted on Echinobase ([link][1]. My tx2name dataframe looks like this: > head(tx2gene) # A tibble: 6 x 3 TXNAME GENEID ntx ...
written 7 months ago by d-joester20
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tximport: Error in medianLengthOverIsoform
... Hi, I am very new to RNAseq, bioconductor, and R. So far, I have successfully established my workflow for DGE of my data, using Salmon, to create transcript-level count tables; tximport, and DESeq2 to aggregate and perform gene level analysis. The following code works as expected: samples < ...
dexseq deseq2 tximport written 7 months ago by d-joester20

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