User: Sebastian Hesse

gravatar for Sebastian Hesse
Reputation:
190
Status:
Trusted
Location:
Germany / Munich / Dr. von Hauner Children's Hospital
Scholar ID:
Google Scholar Page
Last seen:
an hour ago
Joined:
2 years, 1 month 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 • 31 results • page 1 of 4 • next >
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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 6 days ago by Sebastian Hesse190
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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 18 days ago by Sebastian Hesse190
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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 18 days ago by Sebastian Hesse190
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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 12 weeks ago by Sebastian Hesse190 • updated 18 days ago by Papyrus540
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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 12 weeks ago by Sebastian Hesse190
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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 6 months ago by Sebastian Hesse190
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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 6 months ago by Sebastian Hesse190
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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 6 months ago by Sebastian Hesse190
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Comment: A: Usage of selectLab in PCAtools, R
... Thanks for your answers, unfortunately it doesn't work. Maybe I am wrong to assume that I can use the option to label only some of the data-points in the PCA? If I hand it a character vector with just a few of the row names from my metadata it doesn't work though but instead disables all labels. I ...
written 6 months ago by Sebastian Hesse190
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Usage of selectLab in PCAtools, R
... Hi guys I just can not figure out how to use the selectLab option in the biplot of PCAtools. I tried creating a logical vector (withF for every sample I don't want to have a lab for) as well as a vector with all the sample_ids that should have a label. But nothing works nd I can't wrap my head aroun ...
R pcatools written 6 months ago by Sebastian Hesse190

Latest awards to Sebastian Hesse

Teacher 3 days ago, created an answer with at least 3 up-votes. For A: Usage of selectLab in PCAtools, R
Good Question 12 weeks ago, asked a question that was upvoted at least 5 times. For Fold change - a final explanation
Popular Question 12 weeks 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 12 weeks ago, created a post with more than 5 votes. For Fold change - a final explanation
Great Question 4 months ago, created a question with more than 5,000 views. For Fold change - a final explanation
Popular Question 4 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 4 months ago, asked a question with at least 3 up-votes. For Fold change - a final explanation
Popular Question 5 months ago, created a question with more than 1,000 views. For removeBatchEffect with or without log2 values
Scholar 6 months ago, created an answer that has been accepted. For A: Usage of selectLab in PCAtools, R
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.
Great Question 12 months ago, created a question with more than 5,000 views. For Fold change - a final explanation
Epic Question 12 months ago, created a question with more than 10,000 views. For Fold change - a final explanation
Popular Question 18 months ago, created a question with more than 1,000 views. For PVCA message: boundary (singular) fit: see ?isSingular
Popular Question 21 months ago, created a question with more than 1,000 views. For Fold change - a final explanation

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