User: andrew.gehrke

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Posts by andrew.gehrke

<prev • 10 results • page 1 of 1 • next >
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Answer: A: custom background list for ReactomePA
... Thanks for the response Lluis.  Just so im clear, it should work with this? pathway2 <- enrichPathway(gene, universe = c("G1", "G2", "G3")) It seems like no matter what I put in the universe section I always get an error that says  No gene set have size > 10 ... --> return NULL... Do y ...
written 9 months ago by andrew.gehrke0
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custom background list for ReactomePA
... Hi Guangchuang, Is there a way to create a custom universe for the enrichPathway function?  I am using a non-model organism and want to use only the human genes that my organism possesses as the background.  In general im not sure how to use the universe flag, could you provide any help here? Than ...
chipseeker reactomepa guangchuang yu written 9 months ago by andrew.gehrke0
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Answer: A: custom annotation in annotatePeak
... Thank you for the quick response! Everything working great I appreciate it! -Andrew ...
written 9 months ago by andrew.gehrke0
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custom annotation in annotatePeak
... Hi Guangchuang, Is there a way to control annotations in the the annotatePeak function?  For instance I would like to ignore "downstream" and consider those peaks "intergenic".  Or for instance combine "1st exon" with "other exon" so there is one category of "exon".   Any help would be great, than ...
chipseeker guangchuang yu written 9 months ago by andrew.gehrke0
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Answer: A: Diffbind heatmap color change
... As always, thank you very much for your help and prompt response!! -Andrew ...
written 14 months ago by andrew.gehrke0
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Diffbind heatmap color change
... Hi Rory, Sorry for the mundane question, but I think I used to be able to change the color of heatmaps in Diffbind using col = , and now that doesnt seem to work,  Now I get the following error: > plot(samples_final, col ="blues") Error in dba.plotHeatmap(x, ...) :    argument 2 matches multipl ...
diffbind rory stark written 14 months ago by andrew.gehrke0
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Comment: C: loading dba.plotVolcano in DiffBind
... Hi Rory thanks for the 2.3.13 upload, everything looks great! For the dba.Volcanoplots, is there a way to plot all of the differences between multiple samples?  For example, when I upload data for samples X,Y, Z, set up a contrast and make a volcano plot, it looks like its plotting the differences ...
written 18 months ago by andrew.gehrke0
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Comment: C: loading dba.plotVolcano in DiffBind
... Great thanks so much, ive got things working!   Ive noticed though that in figure 7 of the new DIffbind Vignette shows "significant differential bound sites shown in red".  However when I look at the legend, it has the red values listed as FDR > 0.05, while the blue dots are < 0.05.  Is it po ...
written 18 months ago by andrew.gehrke0
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Comment: C: loading dba.plotVolcano in DiffBind
... Hi Rory, Thanks for the prompt response!  When trying to install DiffBind_2.3.12 as you instructed, I get the following two error messages: Error in fetch(key) :    lazy-load database '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/DiffBind/help/DiffBind.rdb' is corrupt > libra ...
written 18 months ago by andrew.gehrke0
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loading dba.plotVolcano in DiffBind
... I noticed a new vignette posted for DiffBind, which now includes an awesome option to plot data as a volcano plot.  I would love to use this, but I cant seem to access this option in DiffBind even when updating the package.   Could you please advise the best way to import the dba.plotVolcano option ...
chipseq diffbind atac-seq rory stark written 18 months ago by andrew.gehrke0 • updated 18 months ago by Rory Stark2.5k

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