User: Sebastian Hesse

gravatar for Sebastian Hesse
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

<prev • 33 results • page 1 of 4 • next >
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Answer: A: Selection Of Background Gene Set In Enrichment Analysis
... 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 Hesse200
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ANOVA and TUKEYs post-test for 3 groups in R
... 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 ...
R expression written 5 weeks ago by Sebastian Hesse200 • updated 5 weeks ago by ATpoint46k
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Comment: C: Weights in normalizeCyclicLoess (Limma, R)
... 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 Hesse200
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Answer: A: Data processing order: normalisation or batch effect correction first?
... 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 Hesse200
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Data processing order: normalisation or batch effect correction first?
... 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 ...
R batch_effect limma proteome written 4 months ago by Sebastian Hesse200
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Correlating metadata with expression based k-means cluster (in R)
... 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 ...
R k-means clustering written 6 months ago by Sebastian Hesse200 • updated 4 months ago by Papyrus690
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Answer: A: Top Variable DEGs into a heatmap
... 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 Hesse200
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Answer: A: Usage of selectLab in PCAtools, R
... [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 Hesse200
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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 Hesse200
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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 Hesse200

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
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Fold change - a final explanation
Popular Question 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 6 months ago, created a post with more than 5 votes. For Fold change - a final explanation
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, asked a question with at least 3 up-votes. For Fold change - a final explanation
Popular Question 9 months ago, created a question with more than 1,000 views. For removeBatchEffect with or without log2 values
Scholar 9 months ago, created an answer that has been accepted. For A: Usage of selectLab in PCAtools, R
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Great Question 16 months ago, created a question with more than 5,000 views. For Fold change - a final explanation
Epic Question 16 months ago, created a question with more than 10,000 views. For Fold change - a final explanation
Popular Question 22 months ago, created a question with more than 1,000 views. For PVCA message: boundary (singular) fit: see ?isSingular
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Fold change - a final explanation

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