User: aurelien

gravatar for aurelien
aurelien10
Reputation:
10
Status:
New User
Location:
Luxembourg
Last seen:
2 years, 2 months ago
Joined:
4 years, 4 months ago
Email:
a****************@uni.lu

Bioinformatic support at the Life Sciences Research Unit, University of Luxembourg

 

 

Posts by aurelien

<prev • 5 results • page 1 of 1 • next >
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pvalRRHO() does not compute the p-value
... Dear RRHO's developer, thanks for developing such a useful package. I am no issue creating the RRHO heatmap, but when computing the p-value using pvalRRHO() the resulting p-value is always 0 regardless of the lists I used or the number of permutations. The scatterplots on the other side make sense ...
pvalue rrho rank written 4.2 years ago by aurelien10
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Comment: C: rounding issues using the VSN package
...     Dear Wolfgang, this is a good idea, the resulting scatter plot looks like: You might be interested in the density of the difference between the two qvalues  the code was added to github. I am sorry, I cannot upload the full results file as they are not mine and part of a PhD study. I do ...
written 4.4 years ago by aurelien10
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Comment: C: rounding issues using the VSN package
...   Dear Wolfgang, thanks again for your kind help.  I was feeding limma with unnormalised abundances just to narrow down the origin of the discrepancy I was observing. Actually, I have a shiny server that run under debian to share the results internally, while I wrote scripts on mac. That is how I ...
written 4.4 years ago by aurelien10
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Comment: C: rounding issues using the VSN package
...   Dear Wolfgang, thanks again for your help. In the tables I first provided, both were processed with vsn2, the numbers are indeed very close, but at the scale of the whole dataset, when we applied a cut-off on the q-values we did not retain the same number of proteins depending on the platform. ...
written 4.4 years ago by aurelien10
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rounding issues using the VSN package
... Dear all, I am using the R package VSN for normalising proteomics data (abundances) that then goes in limma for contrast analysis. I know that VSN was not designed to work with proteomics data but actually vsn2 is doing a great job and clearly stabilised the variance, see below The issue I have, ...
limma vsn2 written 4.4 years ago by aurelien10 • updated 4.4 years ago by Wolfgang Huber13k

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