User: Russ Fraser

gravatar for Russ Fraser
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Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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5 months, 1 week ago
Joined:
11 months, 2 weeks ago
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r*******@uoguelph.ca

Posts by Russ Fraser

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Gviz GenomeAxisTrack Annotation
... Very basic question regarding the annotation of a GenomeAxisTrack in gviz using add53 and add35. It looks like both strands have a 5' on the left, and a 3' on the right. It appears that way in my plots, as well as in the Dec 5, 2017 version of the documentation (p16). Shouldn't the bottom (reverse) ...
gviz written 7 months ago by Russ Fraser0 • updated 7 months ago by Robert Ivanek530
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Comment: C: R Gviz ideogram custom track
... Putting this as a comment rather than answer, because I can't explain why it works... Adding more data to your bands dataframe seems to do the trick: chrom chromStart chromEnd name gieStain scaffold_1 1 7801961 test1 gpos25 scaffold_10 1 2993488 test10 gpos25 scaffold ...
written 9 months ago by Russ Fraser0
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Comment: C: Effect of lfcThreshold on p-value in DESeq2
... Much clearer. Thanks for the detailed explanation! I will lower the lfcThreshold - was just using 2 as it provided an extreme illustration of the effect.   ...
written 9 months ago by Russ Fraser0
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Effect of lfcThreshold on p-value in DESeq2
... I'm having a bit of trouble understanding how lfcThreshold parameter of the results function of DESeq2 affects the p-value. Imposing a stricter lfcThreshold reduces the number of significant results, which makes sense, however, it does so above and beyond what I would have expected. From my data: ...
rnaseq deseq2 statistics written 9 months ago by Russ Fraser0 • updated 9 months ago by James W. MacDonald46k
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Comment: C: Time course analysis in DESeq2: handling common baseline for two experimental co
... I've been following this thread as I have some similar data that I'm wrestling with. With regards to the lfcShrink Wald test p-value, I think you passed the wrong DESeqResults object to the res parameter of lfcShrink. Instead of resday10.shr <- lfcShrink(dds=dds, contrast=c("group", "injury_10 ...
written 9 months ago by Russ Fraser0
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Comment: C: Pheatmap clustering and row annotation
... I tried recreating the issue and the heatmap was generated without a problem. What version of R and pheatmap are you using?   ...
written 9 months ago by Russ Fraser0
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Comment: C: Troubleshooting a histogram DataTrack in Gviz
... Although I couldn't find the answer to my question, I was able to perform a workaround. In short, I imported the VCF as a dataframe into R, keeping only chromosome and position info (cols 1 and 2). I then used the hist function to create breaks and counts of my data. This info can be accessed as fo ...
written 11 months ago by Russ Fraser0
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Troubleshooting a histogram DataTrack in Gviz
... Hello all, I would like to add a track to my Gviz plot that displays the frequency of variants in a specified region. E.g., I have the structure of Gene A, including exons and introns, and I want to quickly visualize how many variants are present in (arbitrarily defined) 100 bp bins along this gene ...
variantannotation gviz written 11 months ago by Russ Fraser0

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