User: david.wheeler7

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Posts by david.wheeler7

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Comment: C: Vertical line at A=0, nothing else, on MA plot
... Thanks Michael! I was running it in Jupyter Notebook and did not see anything. I will try again from the console. ...
written 4 months ago by david.wheeler720
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Comment: C: Vertical line at A=0, nothing else, on MA plot
... Yes!!!! That did it!!! I do not understand the source of the error. If you have time, could please direct me toward the resources need to explain this? Thanks again Michael! ...
written 4 months ago by david.wheeler720
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Comment: C: Vertical line at A=0, nothing else, on MA plot
... Thanks Michael, Sure. here is the output from `res` after changing the order to ` results(dds, contrast=c("group","653","Control"))` log2 fold change (MLE): group 653 vs Control Wald test p-value: group 653 vs Control DataFrame with 246300 rows and 6 columns ...
written 4 months ago by david.wheeler720
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Vertical line at A=0, nothing else, on MA plot
... Hello! I am trying to generate an MA plot with the following code: dds <- DESeq(dds) res = results(dds, contrast=c("group","Control","653")) resultsNames(dds)# this returns 'Intercept' 'group_653_vs_111' 'group_Control_vs_111' plotMA(res, ylim = c(-5, 5)) This returns a pl ...
deseq2 written 4 months ago by david.wheeler720 • updated 4 months ago by Michael Love24k
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Comment: C: How do I prevent my R kernel (Jupyter Notebook) from dying after running varianc
... I just tried the same code in R proper, straight from the console. This was the output: > vsd <- vst(dds, blind = FALSE) `*** caught segfault *** address 0x18, cause 'memory not mapped'` `Traceback:` ` 1: fitDisp(ySEXP = ySEXP, xSEXP = xSEXP, mu_hatSEXP = mu_hatSEXP, log_alphaSEX ...
written 4 months ago by david.wheeler720
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Comment: C: How do I prevent my R kernel (Jupyter Notebook) from dying after running varianc
... Samples = 9, transcripts = 246300. I am not sure what constitutes small here. This is what I have: 16 GB | 2 memory slots, each of which accepts a 2400 MHz DDR4 memory module. Is that too small? Thanks again! ...
written 4 months ago by david.wheeler720
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How do I prevent my R kernel (Jupyter Notebook) from dying after running variance stabilizing transformation?
... Hello! I am following this vignette: http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html. Everytime I run the below code to stabilize the variance: `vsd <- vst(dds, blind = FALSE)` I receive this message: "Kernel Restarting The kernel app ...
deseq2 written 4 months ago by david.wheeler720 • updated 4 months ago by Michael Love24k
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Answer: C: How to reconfigure Jupyter Notebook to locate specific version of R?
... I think you figured it our Vincent! The version command via JN now works and provided the current R which we installed. I will try some packages tomorrow morning and report back. Thanks! ...
written 4 months ago by david.wheeler720
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Comment: C: How to reconfigure Jupyter Notebook to locate specific version of R?
... Thanks Vincent! I found the file! To find the absolute path for R is it correct that I should not use getwd() but instead find the app then use command+i? For me this means that it is "Macintosh HD/Applications/R" Sorry for the rookie questions ...
written 4 months ago by david.wheeler720
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How to reconfigure Jupyter Notebook to locate specific version of R?
... How does one make Jupyter notebook use a specific version of R? - I have had some issues with running DESeq2 via Jupyter Notebook from Anaconda (https://support.bioconductor.org/p/118241/) - We recently downloaded a separate version of R from CRAN (not via Anaconda). This version has none of the ...
deseq2 software error written 4 months ago by david.wheeler720

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