User: alexgraehl

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alexgraehl20
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Posts by alexgraehl

<prev • 17 results • page 1 of 2 • next >
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Comment: C: Limma example where one comparison gives different results depending on the matr
... (I guess that's what the ?contrasts.fit explanation is, I just didn't understand that it would have appreciable effects on a small dataset.) ...
written 12 days ago by alexgraehl20
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Comment: C: Limma example where one comparison gives different results depending on the matr
... Thanks a lot for the explanation! Very good to know. I guess in a perfect world, this would be in the limma documentation (maybe it already is, actually), but thanks again for explaining it. ...
written 12 days ago by alexgraehl20
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Limma example where one comparison gives different results depending on the matrix formulation
... Hi fellow Limma fans,  I can't imagine that this is actually a bug, but is is a REALLY odd situation in which one contrast give me different results depending on how it is formulated.  If you (like me) have been assuming that it doesn't matter if you make your limma design matrix with an explicit ...
limma written 13 days ago by alexgraehl20 • updated 13 days ago by Gordon Smyth35k
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CRISPRseek R package: description of output fields that are unclear
... Hi,  CRISPRSeek, an R package for finding suitable guide RNAs (sgRNAs) for CRISPR targeting, has a lot of output files with partially-undocumented column names. These things may be obvious to a CRISPR expert, but for me, some of the columns are still a mystery.  If anyone else has observations abo ...
crisprseek R sgrna crispr written 2.6 years ago by alexgraehl20 • updated 2.6 years ago by Julie Zhu3.8k
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Q: I notice that there are two terms used: gRNAefficacy calculategRNAEfficacy calculategRNAEfficiency These both appear in the documentation, and are of course both possible valid words! I am assuming that one of these is a typo, and that "efficiency" is the preferred terminology? ...
written 2.9 years ago by alexgraehl20
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... I end up with this error result (see bold part below). I assume this has something to do with filenames / connections, but I'm not sure what exactly causes this error. Possibly next time I will run the script with "options(error=recover)" to try to diagnose it. This is a very long-running job, thoug ...
written 2.9 years ago by alexgraehl20
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Comment: C: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Thanks for the comment! I totally agree that it is worth being not overly-optimistic about the chances of successfully running not-updated packages. In this particular case, I was also wary of this old package, but manual installation of Vienna + GeneRfold + data.table + GeneR actually did seem (at ...
written 2.9 years ago by alexgraehl20
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Current status: even with 4 2 GHz Xeon cores running over the weekend, but after 3 days, not much headway has been made on my 2 megabase region of interest. Maybe this region is just way too big to be even remotely reasonable? I ran CRISPRSeek with multicore enabled, and each of the four multi-core ...
written 2.9 years ago by alexgraehl20
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Answer: A: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... Current status: even with 4 2 GHz Xeon cores running over the weekend, but after 3 days, not much headway has been made on my 2 megabase region of interest. Maybe this region is just way too big to be even remotely reasonable? I ran CRISPRSeek with multicore enabled, and each of the four multi-core ...
written 2.9 years ago by alexgraehl20
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Comment: C: CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for
... I will do that, thanks! It appears that GeneRFold also has a dependency on Vienna: configure: error: viennaRNA library >= 1.5 requiered http://www.tbi.univie.ac.at/~ivo/RNA/ ERROR: configuration failed for package 'GeneRfold' * removing '/usr/lib64/R/library/GeneRfold' ...
written 2.9 years ago by alexgraehl20

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