User: Sebastian Hesse

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30
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New User
Location:
Germany / Munich / Dr.von Hauner Children's Hospital
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Last seen:
2 weeks, 1 day ago
Joined:
3 months ago
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Posts by Sebastian Hesse

<prev • 9 results • page 1 of 1 • next >
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... 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 ...
written 18 days ago by Sebastian Hesse30
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... 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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... 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 ...
written 19 days ago by Sebastian Hesse30
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... 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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... 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 ...
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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... 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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... 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 ...
written 3 months ago by Sebastian Hesse30
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... 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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