User: casey.rimland

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casey.rimland • 110
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110
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Trusted
Location:
University of Cambridge, National Institutes of Health, Chapel Hill School of Medicine
Last seen:
10 months, 2 weeks ago
Joined:
1 year, 4 months ago
Email:
c************@gmail.com

MD/PhD Student in the NIH Cambridge Scholars program and UNC Chapel Hill School of Medicine. 

Posts by casey.rimland

<prev • 22 results • page 1 of 3 • next >
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Comment: C: How to access normalized data in the NanoStringDiff package?
... I was trying to run it before calling the estNormalizationFactors. Fixed it now and have the output. Thank you bunches!   ...
written 12 months ago by casey.rimland • 110
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Comment: C: How to access normalized data in the NanoStringDiff package?
... Thank you! I just gave the code a try and I got stuck on this step with a warning message: Y_n = sweep(Y, 2, lamda_i, FUN = "-") Warning message: In max(cumDim[cumDim <= lstats]) :   no non-missing arguments to max; returning -Inf Anything I might be doing wrong? The code runs through but the ...
written 12 months ago by casey.rimland • 110
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Comment: C: DESeq2 on NanoString Data
... Sounds reasonable. Thanks so much!! I will let you know how it goes :) ...
written 12 months ago by casey.rimland • 110
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Comment: C: DESeq2 on NanoString Data
... As always thank you so much! I will give this a try and let you know how it goes.  One last question: do you do anything at all with the “positive” and “negative” outputs from the Nanostring? Do you still keep them in the data set? ...
written 12 months ago by casey.rimland • 110
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Comment: C: DeSeq2 on NanoString Data
... Thanks for the quick reply! I have not used RUV before so will have to go take a look at that. Do you use RUV before DESeq()? Or is it your method for normalization before things like PCAs/heatmaps and then you still just give the raw Nanostring counts to DESeq() as you would with RNA-Seq data? I've ...
written 12 months ago by casey.rimland • 110 • updated 12 months ago by Michael Love ♦ 24k
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DESeq2 on NanoString Data
... I was wondering if there has been any more consensus recently on using DESeq2 to perform analyses of NanoString data? I have a NanoString dataset with 506 endogenous genes for four sample groups and was looking for the best way to analyze the data. What if I just wanted to use DESeq2 to be able to ...
deseq2 nanostring written 12 months ago by casey.rimland • 110 • updated 12 months ago by Michael Love ♦ 24k
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How to access normalized data in the NanoStringDiff package?
... I am trying to use NanoStringDiff for differential expression analysis of a nanostring data-set with 506 endogenous genes in the set. I was wondering how/if there is a way to output the normalized data that NanoStringDiff uses to run the differential expression LRT tests? I have been able to run the ...
nanostring nanostringdiff written 12 months ago by casey.rimland • 110 • updated 12 months ago by James W. MacDonald ♦ 50k
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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 15 months ago by casey.rimland • 110
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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 15 months ago by casey.rimland • 110
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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 15 months ago by casey.rimland • 110

Latest awards to casey.rimland

Student 13 months ago, asked a question with at least 3 up-votes. For DESeq2 on NanoString Data
Autobiographer 15 months ago, has more than 80 characters in the information field of the user's profile.
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