User: Sebastian Hesse

Reputation:
30
Status:
New User
Location:
Germany / Munich / Dr.von Hauner Children's Hospital
Scholar ID:
Google Scholar Page
Last seen:
3 weeks, 5 days ago
Joined:
9 months ago
Email:
h**************@googlemail.com

Physician scientist at the Dr. von Hauner Children's Hospital of the LMU Munich.

Interests: Neutrophil granulocytes, primary immunodeficiencies, multi-comics analysis, proteomics, transcriptomics, whole exome sequencing 

 

 

Posts by Sebastian Hesse

<prev • 15 results • page 1 of 2 • next >
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Comment: C: eBayes(fit_object, trend = T) gives: Error in fitFDist(var, df1 = df, covariate
... Shame on me! It gave: ``` Min. 1st Qu. Median Mean 3rd Qu. Max. NA's 10.60 14.31 15.35 15.69 16.69 26.57 45 ``` So there were NAs, I just didn't look hard enough. I removed them using: prots_with_NA <- which(apply(exprs(eSet_log2), 1, function(x) any ( is.na(x))) ...
written 5 months ago by Sebastian Hesse30 • updated 5 months ago by Gordon Smyth38k
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Comment: C: eBayes(fit_object, trend = T) gives: Error in fitFDist(var, df1 = df, covariate
... If you are interested and willing to check out the original dataset I would be happy to invite you to the dropbox with the data and markdowns. ...
written 5 months ago by Sebastian Hesse30
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Comment: C: eBayes(fit_object, trend = T) gives: Error in fitFDist(var, df1 = df, covariate
... I have no NAs anywhere and all other options (trend=F, robust=T) run without problems. ...
written 5 months ago by Sebastian Hesse30
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Comment: C: VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
... Is it maybe an option to use the log2 matrix and then use either trend = T and/or robust = T ? ...
written 5 months ago by Sebastian Hesse30
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eBayes(fit_object, trend = T) gives: Error in fitFDist(var, df1 = df, covariate = covariate) : NA covariate values not allowed
... Im performing diff expression analysis for proteome data with LIMMA. As heteroscedasticity is present in my data and could not be corrected with VOOM (question [here][1]) I would like to try eBayes with the option trend = T. Unfortunately I get the error: Error in fitFDist(var, df1 = df, covariate = ...
limma ebayes written 5 months ago by Sebastian Hesse30 • updated 5 months ago by Gordon Smyth38k
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VOOM vs VSN vs log2 to transform proteome data before LIMMA analysis
... I am analysing an proteome dataset, derived from DIA mass spec with quantified values from Biognosys Spectronaut 11, and I would like to use LIMMA for differential expression analysis. Im just a beginner and not very experienced yet so please forgive me if my question isn't perfectly stated. Accord ...
vsn limma R voom written 5 months ago by Sebastian Hesse30 • updated 5 months ago by Wolfgang Huber13k
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ClusterProfiler: what to show as dot size (GeneRatio vs Count)
... Im currently playing with the clusterProfiler output and noticed the different ways of plotting data, either using GeneRatio or Count as the representations in the point size. So far, counts I like the most as they are easiest to understand but I wonder why GeneRatio is the default. Is it more meani ...
clusterprofiler written 6 months ago by Sebastian Hesse30
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Answer: A: Selection of terms in clusterProfiler, the inverse of dropGO
... Ok, I found a workaround: excludeCCdown <- data.frame("ID" = down_CC@compareClusterResult$ID, "name" = down_CC@compareClusterResult$Description) remove <- c("GO:0099503", "GO:0042582", "GO:0042581", "GO:0070820 ", "GO:0101002") #secretory vesicle, azurophil granule, specific granule, ...
written 6 months ago by Sebastian Hesse30
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Selection of terms in clusterProfiler, the inverse of dropGO
... The clusterProfiler package has the function dropGO to exclude terms from the plotting but is there also a method so select the terms one wants to show? Im asking because in my cellular component enrichment I have multiple occurrences of eg granule subsets and would specifically choose only non red ...
clusterprofiler R written 6 months ago by Sebastian Hesse30
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Comment: C: Define batch effect variables before removing them or getting rid of hidden surr
... I found a package plotting exactly what I wanted called PVCA. Now the problem arises, that I have quite a lot of candidates for batch effects and I will beed to decide which ones to correct for. I opened a new question for that here: https://support.bioconductor.org/p/115278/ Any comments here or a ...
written 9 months ago by Sebastian Hesse30

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