User: sven.schenk

gravatar for sven.schenk
sven.schenk10
Reputation:
10
Status:
New User
Location:
Vienna
Last seen:
6 months ago
Joined:
1 year, 5 months ago
Email:
s**********@univie.ac.at


 

Posts by sven.schenk

<prev • 16 results • page 2 of 2 • next >
0
votes
1
answer
272
views
1
answer
comparing two GOstats result lists
... Hi, I am trying to compare two result lists from GOstats. The reason for doing this is that I did a proteomics experiment in which we established a new sample preparation protocol and I now want to kind of show that with this new method we do not enrich/deplete for certain proteins/protein function ...
gostats statistics written 16 months ago by sven.schenk10 • updated 16 months ago by James W. MacDonald51k
0
votes
2
answers
383
views
2
answers
Comment: C: GO Stats results contain GO terms NOT present in the gene universe
... hi,   thanks for your answer. i came to the same conclusion, when checking what`s happening during building the GOallframe - in this I have something like 4700 Go terms insteadt of 2472 in my input list. so it was indeed a misunderstanding how GOstats works. thanks again for the answer and the ad ...
written 17 months ago by sven.schenk10
0
votes
2
answers
383
views
2
answers
Comment: C: GO Stats results contain GO terms NOT present in the gene universe
... hi again, sorry for not using the COMMENT/REPLY button. no, i did not just update GO.db, i updated the whole installation from 3.3.2 to 3.5.0 it wouldn't work otherwise. yes, you're right that it would be expected that i find more non-matching GO terms if i use a newer DB, however, even if i use a ...
written 17 months ago by sven.schenk10
0
votes
2
answers
383
views
2
answers
Answer: A: GO Stats results contain GO terms NOT present in the gene universe
... hi, thanks for your answer. so i updated my GO.db from 3.3.0 to 3.6.0 and rerun the analysis, however the problem persits (it even gets more pronounced). so i think the problem is the time of annotaion of my transcriptome which was in July 16 and my old GO.db (3.3.0) was form October 16 wich led to ...
written 17 months ago by sven.schenk10 • updated 17 months ago by Martin Morgan ♦♦ 23k
0
votes
2
answers
383
views
2
answers
Comment: C: GO Stats results contain GO terms NOT present in the gene universe
... addendum: my GOStats code would look something like this: >goFrame_gU.new.H = GOFrame(gU_frame.new, organism="Homo sapiens") >goALLFrame.gU.new.H = GOAllFrame(goFrame_gU.new.H) >ids <-c("comp2258926_c0_seq3","comp2258476_c0_seq2","comp2246178_c0_seq1","comp2268190_c1_seq4") >univ ...
written 17 months ago by sven.schenk10
3
votes
2
answers
383
views
2
answers
GO Stats results contain GO terms NOT present in the gene universe
... hi, i used GOstats to check for over and under represented GO terms in my gene lists using a conditional test. i then combined the three output files, i.e. the files for MF, BP and CC, into one list containing 175 under represented terms: > head(GO.Mat,2) GOBPID Pvalue OddsRatio ExpC ...
gostats written 17 months ago by sven.schenk10 • updated 17 months ago by emmascottgm0

Latest awards to sven.schenk

Autobiographer 16 months ago, has more than 80 characters in the information field of the user's profile.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 228 users visited in the last hour