User: casey.rimland

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University of Cambridge, National Institutes of Health, Chapel Hill School of Medicine
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MD/PhD Student in the NIH Cambridge Scholars program and UNC Chapel Hill School of Medicine. 

Posts by casey.rimland

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Can Tximport average transcript length be used for GOSeq?
... I am pretty confident I included correctly the DE genes n the second plot as the number of "True"/"1" is equal to the number of differentially expressed genes in the list I imported... To get this list, I have been taking an overlap of genes significantly up-regulated in Tissue C when compared to ei ...
written 28 days ago by casey.rimland • 70
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Comment: C: Unmix() function in DeSeq capabilities
...   Hmm... Maybe?  Let me explain a bit more about what we have to see if that might make sense to consider...: We took three different human tissues A, B, C and with these tissues we mechanically dissociated the epithelial cells (scraped them off with a scalpel blade). This gave us about a 90-95%i ...
written 29 days ago by casey.rimland • 70
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Comment: C: Can Tximport average transcript length be used for GOSeq?
... Yea, I am still at the learning R stage where I tend to be very very inefficient with my code :D! I have edited the above post with updated code and made it much more efficient. In my "banging my head" state yesterday I did a ton of rather useless steps I now realize.  The pwf plots are still look ...
written 29 days ago by casey.rimland • 70
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Unmix() function in DeSeq capabilities
... I saw a recent post by Michael Love (https://support.bioconductor.org/p/107157/#107197) about the DeSeq2 function unmix() and I had a follow-up question (but did not want to hijack the original poster's question with one of my own.) Could unmix() be used if you only know the expression profile of o ...
deseq2 written 29 days ago by casey.rimland • 70 • updated 28 days ago by Michael Love ♦ 17k
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Comment: C: Interpreting heatmap in DESEQ2
... No problem, it was kinda cool to realize I actually knew something for once :D! ...
written 29 days ago by casey.rimland • 70
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Answer: A: Interpreting heatmap in DESEQ2
... Row Z-Score is a scaling method for visualization in heat maps that helps enhance clusters of genes with similar trends in expression between samples. Z-Score is calculated by: (Gene expression value in sample of interest) - (Mean expression across all samples) / Standard Deviation   In the heat ...
written 4 weeks ago by casey.rimland • 70
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Comment: A: Can Tximport average transcript length be used for GOSeq?
... Thanks for the reply Steve! So I spent literally all day trying to figure out how to go about doing that, now that I know its okay...and I think maybe I finally figured it out? Getting the data into the right format for GOseq is a bit of a beast for a novice R user!! Any chance you're feeling supe ...
written 4 weeks ago by casey.rimland • 70
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Can Tximport average transcript length be used for GOSeq?
... I’m trying to run GOSeq with human RNA Seq data that has been processed with Salmon, summarized to gene level with tximport, and DGE run using DeSeq2.  I was reading the vignette for GOSeq and got stuck/confused on the part where you need to know what human genome build you used... It says you need ...
goseq deseq2 tximport written 4 weeks ago by casey.rimland • 70
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DeSeq2 with three groups which approach to use? LRT or just do multiple pairwise comparisons?
... I have a question about the best approach for analyzing an RNA-Seq experiment using DeSeq2. My experiment involves three different tissue types (named C, G, and P). I want to find out what genes are enriched in/unique to  each tissue in comparison to the other two tissues. What I was not sure of is ...
deseq2 written 9 weeks ago by casey.rimland • 70 • updated 9 weeks ago by Michael Love ♦ 17k
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Comment: C: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
... Also I forgot to mention that your vivid description of how your biologist colleagues would ask about the duplicates made me chuckle. hehe, I would totally come to you and say: 'wassup with all these dups'! Thanks again for taking the time to answer :D ...
written 11 weeks ago by casey.rimland • 70

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