User: casey.rimland
casey.rimland • 130
- Reputation:
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- Location:
- University of Cambridge, National Institutes of Health, Chapel Hill School of Medicine
- Last seen:
- 1 year, 2 months ago
- Joined:
- 1 year, 8 months ago
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- c************@gmail.com
MD/PhD Student in the NIH Cambridge Scholars program and UNC Chapel Hill School of Medicine.
Posts by casey.rimland
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... I was trying to run it before calling the estNormalizationFactors. Fixed it now and have the output. Thank you bunches!
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written 16 months ago by
casey.rimland • 130
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... 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 16 months ago by
casey.rimland • 130
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C: DESeq2 on NanoString Data
... Sounds reasonable. Thanks so much!! I will let you know how it goes :)
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written 16 months ago by
casey.rimland • 130
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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?
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written 16 months ago by
casey.rimland • 130
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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 16 months ago by
casey.rimland • 130
• updated
16 months ago by
Michael Love ♦ 25k
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... 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 ...
written 16 months ago by
casey.rimland • 130
• updated
16 months ago by
Michael Love ♦ 25k
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... 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 ...
written 16 months ago by
casey.rimland • 130
• updated
16 months ago by
James W. MacDonald ♦ 51k
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... 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 19 months ago by
casey.rimland • 130
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...
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 19 months ago by
casey.rimland • 130
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... 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 19 months ago by
casey.rimland • 130
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For DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
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