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Different results between LOLAweb interactive server and local R package #27
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They should be the same. What kind of differences are you seeing? |
the most significant enrichment (a USCS feature table) in web-based LOLA is not significant at all in local R version. web-based UCSC switchDbTss result (pValueLog is infinity):
local R package UCSC switchDbTss result: I manually check the overlap between my regions and switchDbTss using findOverlaps function in R, and it seems the local version is right, there is not too many overlaps. |
Have you run this on the most recent version of lolaweb? can you try re-running it to see what happens? can you send me the link to the results on lolaweb? |
the d value is very different in your analyses which tells me the universe may be different. what reference genome assembly are you using? and what universe are you using? |
I just re-run LOLAweb with my own universe and you can see the results from
http://lolaweb.databio.org/?key=W352OUYCHGVAK48
I also re-run LOLA in R and still see the difference. Input files, command
and results are here
https://drive.google.com/drive/folders/19pkIsQKCueKyqQh3OqqGa2vhhpMM29hs?usp=sharing
The universe I am using is a 1kb tiles hg19 bed file made by myself. I have
tried LOLAweb with premade universe tills1000.hg19.bed and my own 1kb tiles
hg19 universe. Both of them give me almost the same results, but different
with local R version.
Thank you for your help!
…On Wed, Apr 25, 2018 at 2:42 PM, Nathan Sheffield ***@***.***> wrote:
the d value is very different in your analyses which tells me the universe
may be different. what reference genome assembly are you using? and what
universe are you using?
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that is strange if you're using the same universe in both places. I will have to see if I can reproduce this. thanks for the files I'll take a look. |
Thanks!
…On Wed, Apr 25, 2018 at 4:02 PM, Nathan Sheffield ***@***.***> wrote:
that is strange if you're using the same universe in both places. I will
have to see if I can reproduce this. thanks for the files I'll take a look.
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I got different results from LOLAweb interactive server and LOLA installed from bioconductor with the same input files( region set, universe, and core database). What's the difference between web-based LOLA and LOLA R package?
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