Comments (7)
nsheff
commented on July 24, 2024
They should be the same. What kind of differences are you seeing?
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NyxSLY
commented on July 24, 2024
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):
| userSet | dbSet | collection | pValueLog | oddsRatio | support | rnkPV | rnkLO | rnkSup | maxRnk | meanRnk | b | c | d | description | cellType | tissue | antibody | treatment | dataSource | filename | size | id | axis_label |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| allCT_regions.bed | 3011 | ucsc_features | 25.14260683 | 470 | 1 | 76 | 10 | 76 | 29 | 112178 | 458 | 2748406 | UCSC Switch DB TSSs | switchDbTss.bed | 131780 | UCSC Switch DB TSSs_3011 | UCSC Switch DB TSSs |
local R package UCSC switchDbTss result:
userSet dbSet collection pValueLog logOddsRatio support rnkPV rnkLO rnkSup maxRnk meanRnk b c d description cellType tissue antibody treatment dataSource filename qValue size
1 3011 ucsc_features 0.432783493920793 1.06557508871529 40 796 867 203 867 622 112504 995 2982142 UCSC Switch DB TSSs NA NA NA NA NA switchDbTss.bed 1 131780
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.
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nsheff
commented on July 24, 2024
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?
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nsheff
commented on July 24, 2024
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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NyxSLY
commented on July 24, 2024
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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nsheff
commented on July 24, 2024
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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NyxSLY
commented on July 24, 2024
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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Related Issues (20)
- hg38 database HOT 1
- Add in missing cellType/antibody entries for encodeTFBSmm10 HOT 6
- Re-order result columns
- Inclusion of mm10 JASAPR prediction track into LOLA JASPAR HOT 3
- cistrome_mm10 HOT 2
- runLOLA results table for PEP databases
- PEP file read caching HOT 2
- Can't load an example regionDB. HOT 3
- PEP tag system
- testing for enrichment of significant individual cpgs HOT 2
- Error if GRangesList has names HOT 2
- question: how to test two region sets for differential enrichment with buildRestrictedUniverse? HOT 2
- Each of the 2 combined objects has sequence levels not in the other: HOT 4
- R package error HOT 4
- LOLA runLOLA-regionDB to use for tissue-specific TFBS
- P4 tool not grouping according to the paper!!
- Error by using extractEnrichmentOverlap function
- Fisher test - two sided hypothesis
- Error when trying to load a regionDB
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