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User: JWCarlson

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JWCarlson70
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Posts by JWCarlson

<prev • 11 results • page 1 of 2 • next >
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... Yes. It's a strange thing. When I look at showClass("DESeqDataSet"), NAMES is charcterORNULL. But your results show that it is character_OR_NULL. I agree that from all appearances, my initialization of DESeqDataSet looks like it's pulling in an older version of S4Vectors. I've stepped through the i ...
written 21 months ago by JWCarlson70
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... Thanks for your work on this Michael. This is what I upgraded: > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21). Old packages: 'Biobase', 'BiocParallel', 'GenomicRanges', 'SummarizedExperiment' I updated all. If I take ou ...
written 21 months ago by JWCarlson70
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... I recognize that my setClassUnion call is a hack. It's a workaround until this gets sorted out and something to convince me that this really is the issue. In answer to your questions, the constructor works and it shows character_OR_NULL. (As does RangedSummarizedExperiment; DESeqDataSet show NAMES ...
written 21 months ago by JWCarlson70
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... I'm starting to get more suspicious of the change in the S4Vectors package. Renaming characterORNULL to character_OR_NULL happened in 0.14.0 9 days ago. What is your version of S4Vectors? ...
written 21 months ago by JWCarlson70
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... so this does not look right. > showClass("DESeqDataSet") Class "DESeqDataSet" [package "DESeq2"] Slots: <lines deleted> Name: assays NAMES Class: Assays characterORNULL <more lines deleted> > showClass("Ran ...
written 21 months ago by JWCarlson70
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Comment: C: DESeqDataSetFromTximport: Error in checkSlotAssignment
... sure! > dds=makeExampleDESeqDataSet() Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot 'NAMES' in an object of class "DESeqDataSet"; is(value, "characterORNULL") is not TRUE > traceback() 11: stop(gettextf("assignment of an o ...
written 21 months ago by JWCarlson70
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Comment: A: DESeqDataSetFromTximport: Error in checkSlotAssignment
... Incidentally, I see that makeExampleDESeqDataSet() also returns the same error for me > dds = makeExampleDESeqDataSet() Error in checkSlotAssignment(object, name, value) : assignment of an object of class "NULL" is not valid for slot 'NAMES' in an object of class "DESeqDataSet"; is(value, "char ...
written 21 months ago by JWCarlson70
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Comment: A: DESeqDataSetFromTximport: Error in checkSlotAssignment
... Hi Michael, Thanks for the response. biocLite() looks clean: > biocLite() BioC_mirror: https://bioconductor.org Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21). For a brief time, I thought my problem was that I was no pulling in tximportData. But adding that did not help. ...
written 21 months ago by JWCarlson70
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DESeqDataSetFromTximport: Error in checkSlotAssignment
... I'm wrestling with tximport/DESeq2. I've create a small experiment dataset of 2 paired end fastq, generated counts with salmon, and successfully read them in with tximport (or so I think). "files" is my list of 2 quant.sf files. tx2gene is the obvious. > txi <- tximport(files, type = "salmon ...
deseq2 tximport written 21 months ago by JWCarlson70
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Answer: A: Our mart (on https) is not compatible with biomaRt access. What's wrong?
... That does the trick. the postredir=2L was the part I needed. Thanks! Will there be a future patch that allows for https and dealing with 'document moved' responses? ...
written 2.8 years ago by JWCarlson70

Latest awards to JWCarlson

Popular Question 21 months ago, created a question with more than 1,000 views. For DESeqDataSetFromTximport: Error in checkSlotAssignment
Student 21 months ago, asked a question with at least 3 up-votes. For DESeqDataSetFromTximport: Error in checkSlotAssignment

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