User: hesse.sebastian
hesse.sebastian • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Last seen:
- 2 months, 1 week ago
- Joined:
- 9 months, 1 week ago
- Email:
- h**************@googlemail.com
Posts by hesse.sebastian
<prev
• 20 results •
page 1 of 2 •
next >
0
votes
1
answer
187
views
1
answer
... Im using clusterProfiler for GO enrichment of differentially expressed proteins from different groups.
It appears that most suitable is to use as a background for enrichment all proteins that "potentially could be in the lift of the differentially expressed proteins".
My issue is that I am not 100% ...
written 11 weeks ago by
hesse.sebastian • 80
• updated
11 weeks ago by
Jean-Karim Heriche ♦ 20k
0
votes
1
answer
235
views
1
answers
... Great workaround, thanks! ...
written 3 months ago by
hesse.sebastian • 80
2
votes
1
answer
235
views
1
answer
... In my set of differentially expressed proteins (derived from comparison of different genotypes to healthy) I would like to check if specific GO-terms are enriched (eg. if one set of proteins contains significantly more often the annotation for "membrane" = GO:0016020).
Currently I am using clusterP ...
written 3 months ago by
hesse.sebastian • 80
• updated
3 months ago by
jared.andrews07 • 2.7k
0
votes
1
answer
1.7k
views
1
answers
... Is there something I could/should do about? What I noticed in this particular combination of samples (I am performing proteome analysis with different groups of patients agains a large healthy comparison group) is that "age" is a very strong variance influence. I suppose this has to do with the part ...
written 3 months ago by
hesse.sebastian • 80
0
votes
1
answer
1.7k
views
1
answer
... Running the pvcaBatchAssess from the pvca package I get the message: "boundary (singular) fit: see ?isSingular".
Unfortunately I do not understand this message and also "?isSingular" doesnt help me much.
Can you advice me on what to do?
The function runs through though and I get a graphical output ...
written 3 months ago by
hesse.sebastian • 80
1
vote
0
answers
340
views
0
answers
... Thank you all for your inputs! I made more graphs/calculations and moved the question [here][1]
[1]: https://support.bioconductor.org/p/118495/#118500 ...
written 4 months ago by
hesse.sebastian • 80
2
votes
2
answers
315
views
2
answers
... As VOOM gave strange results that still showed heteroscedasticity I solved it now using log2 values and the LIMMA option `eBayes(fit2_object, trend = F, robust = T) `
Thank you all for your input! ...
written 4 months ago by
hesse.sebastian • 80
1
vote
0
answers
264
views
0
answers
... Working with a proteome dataset I would like to check and correct for batch effects.
For batch effect detection I am using [PVCA][1], for batch effect correction LIMMAS [removeBatchEffect][2].
Data come from DIA proteome analysis, quantified using Biognosys Spectronaut 11, details can be found in ou ...
written 4 months ago by
hesse.sebastian • 80
0
votes
2
answers
315
views
2
answers
... Thanks a lot for your answer ivivek!
I agree with all your points and actually follow them, only the one about doing the diff ex analysis with counts instead of log2 values is puzzling me. I am working with DIA derived quantitative proteome data. So far I always put log2 values into LIMMA for diff ...
written 4 months ago by
hesse.sebastian • 80
5
votes
2
answers
315
views
2
answers
... Using LIMMA's removeBatchEffect and PVCA to check for batch influences before and after removal I just noticed that if I don't use log2 values the batch effect removal does not work in the sense that PVCA shows retained batch effects after removal. With log2 values all runs fine.
Is this a general ...
written 4 months ago by
hesse.sebastian • 80
Latest awards to hesse.sebastian
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Fold change - a final explanation
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1624 users visited in the last hour