User: Sebastian Hesse
Sebastian Hesse • 200
- Reputation:
- 200
- Status:
- Trusted
- Location:
- Germany / Munich / Dr. von Hauner Children's Hospital
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month, 1 week ago
- Joined:
- 2 years, 4 months ago
- Email:
- h**************@googlemail.com
Physician scientist
Reseach focus: Multiomics, Whole exam sequencing
Clinical focus: Pediatrics, Primary Immunodeficiencies, Oncology, Genetics
Posts by Sebastian Hesse
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1
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... I would like to refer this topic and ask if a statistical point could be made?
Couldn't we calculate the effect of different background sizes?
...
written 5 weeks ago by
Sebastian Hesse • 200
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... In a dataset of protein expression values (expression data as log2) we found 3 clusters using k-means.
Now we would like to first perform an ANOVA and next a post-test (eg Tukeys) to test each pair of cluster grouping for differentially expressed proteins.
Unfortunately, no resources I found discus ...
written 5 weeks ago by
Sebastian Hesse • 200
• updated
5 weeks ago by
ATpoint ♦ 46k
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... Still nothing? I just used the function again and checked here if anyone had an idea... but seems that not.
Trying to revive the question with a comment. ...
written 3 months ago by
Sebastian Hesse • 200
0
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1
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195
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1
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... Thanks a lot for your answers!
Im actually using a whole array of normalisations and then then which one stands out as best (eg in numbers of diffEx and clustering algorithms).
Im using:
- clr
- cyclic loess
- VSN
- cubic splines
- quantile normalisation
- median normalisation
So far VSN always ga ...
written 4 months ago by
Sebastian Hesse • 200
1
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1
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195
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1
answer
... There are several questions about this topic but none of them received a clear answer, so here is my try to find a solution:
I am working with a proteome dataset that clearly has a batch effect from the date the MS measurement was done.
The dataset is also not normalised yet.
Now, which is the corr ...
written 4 months ago by
Sebastian Hesse • 200
2
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1
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274
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1
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... I am analyzing the proteome data of cells from patients with different monogenic backgrounds of a specific disease.
For cluster analysis, I applied the k-means algorithm from the stats package and used sum-of-square and silhouette width to determine the optimal amount of clusters. Next, I plotted th ...
written 6 months ago by
Sebastian Hesse • 200
• updated
4 months ago by
Papyrus • 690
1
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2
answers
471
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2
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... You could simply filter the genes by the significance level before running your k-means analysis:
#extract significant results
get_sigs <- function(df, adj.p, FC){
df <- df[df$adj.P.Val < adj.p & abs(df$logFC) >= FC,]
return(df)
}
This is how I reduce my gene/p ...
written 6 months ago by
Sebastian Hesse • 200
3
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1
answer
319
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1
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... [ATpoint][1] and [Kevin Blighe][2] brought the solution!
selectLab expects a character vector with the exact labels we are handing to lab, not the corresponding row names.
If your metadata are factors, labs need as.character(), otherwise it prints the factor levels only.
biplot(data_PCA,
...
written 9 months ago by
Sebastian Hesse • 200
0
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1
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319
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1
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Comment:
C: Usage of selectLab in PCAtools, R
... Ah, ok. This explains it!
It seems that selectLab is expecting the exact labels to include, not the corresponding row names / samples.
If I give selectLab a character vector with all metadata chars to include it works.
Actually it needs a little workaround still with as.character(metadata) as other ...
written 9 months ago by
Sebastian Hesse • 200
0
votes
1
answer
319
views
1
answers
Comment:
C: Usage of selectLab in PCAtools, R
... data_PCA$metadata$genotype contains a character vector that I use as a label.
If I use it without the selectLab option all runs fine but labels are shown for each data point which is a bit overwhelming. Thats why im trying to limit the label just to a few selected points. ...
written 9 months ago by
Sebastian Hesse • 200
Latest awards to Sebastian Hesse
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Selecting the background for GO enrichment analysis (proteomics)
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Design matrix for voom: with or without batch blocking?
Popular Question
3 months ago,
created a question with more than 1,000 views.
For PVCA message: boundary (singular) fit: see ?isSingular
Teacher
3 months ago,
created an answer with at least 3 up-votes.
For A: Usage of selectLab in PCAtools, R
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6 months ago,
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For Fold change - a final explanation
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6 months ago,
created a question with more than 1,000 views.
For Using clusterprofiler (or else) top look for enrichment of one specific GO term
Appreciated
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Great Question
8 months ago,
created a question with more than 5,000 views.
For Fold change - a final explanation
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Using clusterprofiler (or else) top look for enrichment of one specific GO term
Student
8 months ago,
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9 months ago,
created a question with more than 1,000 views.
For removeBatchEffect with or without log2 values
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9 months ago,
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For A: Usage of selectLab in PCAtools, R
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Great Question
16 months ago,
created a question with more than 5,000 views.
For Fold change - a final explanation
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created a question with more than 10,000 views.
For Fold change - a final explanation
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22 months ago,
created a question with more than 1,000 views.
For PVCA message: boundary (singular) fit: see ?isSingular
Popular Question
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For Fold change - a final explanation
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