User: penny.lane

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Posts by penny.lane

<prev • 11 results • page 1 of 2 • next >
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... OK, thanks again Michael. ...
written 14 hours ago by penny.lane0
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... Ah, I see, but do you agree that in the context of this code it's simpler just to relevel the sampleTable from the outset rather than to have to do it twice? Just want to make sure I'm not still misunderstanding something. ...
written 14 hours ago by penny.lane0
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... I had actually tried to implement the relevel approach outlined in the vignette, but it didn't fix mt problem, so I wasn't sure it was actually what I needed to do. However, since you sent me back there I tried modifying my original code. I think the code in the vignette assumes a dds object exists ...
written 15 hours ago by penny.lane0
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... As far as I can tell this is not explained in the tutorials (I have read them). I'd be happy to be wrong about that though, so please point me to where you see it explained and I'll be out of your hair. It does not seem to be a very basic form of analysis and one that could easily be done wrong beca ...
written 17 hours ago by penny.lane0
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Responder Vs Non-Responders Paired Comparison DESeq2
... There was an earlier post that nicely explained how to build a design matrix for a paired responder vs non-repsonder analysis: https://support.bioconductor.org/p/95143/#124666 In that example, the assumption was that there were two conditions, "screen" and "treatment", representing before and after ...
deseq2 written 20 hours ago by penny.lane0 • updated 16 hours ago by Michael Love25k
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Comment: C: Responder Vs Non-Responders Paired Comparison DESEQ2
... In this example, if there were several conditions (instead of just 2), say "before", "during" and "after", how would you specify that you want "before" to be the base case for comparison? It seems like it might be defaulting to alphabetical order, leaving me without "groupY.conditionAfter" and "grou ...
written 3 days ago by penny.lane0
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... Awesome, that did the trick. Thanks so much for the rapid assistance Michael! ...
written 5 days ago by penny.lane0
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... Yup, good thinking on that one. It worked on another machine, so I wiped R and reinstalled all my packages 1-by-1, testing the tximport command after each package I installed. Turns out that as soon as I install the GEOquery package, my tximport command starts malfunctioning (as described above). I ...
written 5 days ago by penny.lane0
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... Well, it's probably not failing because of the whitespace in the folder name at least... I just moved the files to a folder without whitespace and confirmed the problem still exists. Did anything change about the package from Bioconductor 3.8 to 3.9 that could have broken the use of custom column na ...
written 6 days ago by penny.lane0
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... Unfortunately it contains some confidential information, but hopefully this redacted version gives you a sense: [1] "C:\\Users\\Penny Lane\\Documents\\analysis\\company\\cmpd\\clinical_samples\\downsampling\\rsem\\Paxgene\\file1.rsem.genes.results" [2] "C:\\Users\\Penny Lane\\Documents\\analysis\\c ...
written 6 days ago by penny.lane0

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