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User: Sebastian Hesse

Reputation:
30
Status:
New User
Location:
Germany / Munich / Dr.von Hauner Children's Hospital
Scholar ID:
Google Scholar Page
Last seen:
2 weeks, 1 day ago
Joined:
3 months ago
Email:
h**************@googlemail.com

Posts by Sebastian Hesse

<prev • 9 results • page 1 of 1 • next >
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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 18 days 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 19 days 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 19 days 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 3 months ago by Sebastian Hesse30
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Interpretation of PVCA result and what to correct for
... Thanks to PVCA I finally found a tool to check the effect of all my suspected confounders I annotated in my proteome project. But now my problem is that I don't really know what to correct for and what to better leave. https://ibb.co/bUCX4f   First, should I now remove all major effects (eg da ...
pvca batch effect batch effect correction written 3 months ago by Sebastian Hesse30
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Comment: C: ComBat with multiple batches
... Hi ben.run974, did you find a solution yet if this is the correct way? Thanks! Sebastian ...
written 3 months ago by Sebastian Hesse30
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Comment: C: Error in solve.default(t(mod) %*% mod) : Lapack routine dgesv: system is exactl
... Hi Aina, did you find a solution yet? I get the very same error.... Thanks! Sebastian   ...
written 3 months ago by Sebastian Hesse30
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Define batch effect variables before removing them or getting rid of hidden surrogate variables
... Dear community, much has been written and asked on this topic but I'm still a bit confused and would appreciate it very much to get a defined guideline on how to handle batch effects in omics datasets (in my case proteomics but its probably applicable to any). So I do have two data frames, one con ...
proteomics sva batch effect correction written 3 months ago by Sebastian Hesse30
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Comment: C: sva: how to incorporate adjusting variables
... Dear Olivia, dear Jeff, though this thread is a bit dated I am facing the same problem here and maybe Olivia has found and answer since a long time (I certainly hope so for you :) I am wondering how you determined which factors do have an influence on your data in the first place? How can we deter ...
written 3 months ago by Sebastian Hesse30

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