User: mikhael.manurung

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Posts by mikhael.manurung

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Flow cytometry optimization of transformation parameters
... Or you can merge all of your fcs files to get a better estimate of the transformation parameters ```r fs_merge <- flowFrame(fsApply(fset, exprs)) trans <- estimateLogicle(fs_merge, chnls) # apply transformation to your flowSet fset <- trans %on% fset ``` ...
written 6 days ago by mikhael.manurung30
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Comment: C: Useful of Normal Enrichment Score (NES) in GSEA
... You can refer to this post [about GSEA in another forum.][1] I hope it helps. Best, Mikhael [1]: https://www.biostars.org/p/132575/ ...
written 13 days ago by mikhael.manurung30
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Comment: C: Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
... Are the differences in the gene expression biologically plausible? I think it makes sense if a gene is turned on/off depending on the environment/condition. I am not familiar with DESeq2, but with edgeR and limma you can use their robust setting to minimise the effect from outliers to DGE analysis. ...
written 17 days ago by mikhael.manurung30
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Comment: C: Counts Worry: DESeq2: DEGs are from genes with mostly zero across groups
... Are the differences in the gene expression biologically plausible? I think it makes sense if a gene is turned on/off depending on the environment/condition. I am not familiar with DESeq2, but in edgeR and limma you can use their robust setting to minimise the effect from outliers to DGE analysis. ...
written 17 days ago by mikhael.manurung30
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Comment: C: Cydar's countCells tolerance parameter for arcsinh-transformed data
... Dear Aaron, Thank you for taking the time to write such an elaborate reply. Indeed, I asked about the choice for best hypersphere radius and then moved on rather suddenly to minimum cells/hypersphere threshold. At first, I considered ```cydar``` as a completely unbiased method to analyse the cytom ...
written 17 days ago by mikhael.manurung30
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Comment: C: Cydar's countCells tolerance parameter for arcsinh-transformed data
... Dear Aaron, Thank you for the quick response especially for the link to the repository. However, please bear with me as I do not think I have fully understood your answer. You said that the default 0.5 tolerance corresponds to a 10-fold difference of intensities between the opposing edges of the sp ...
written 20 days ago by mikhael.manurung30
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Comment: C: DESeq2 log2FC shrink before GSEA or not?
... I think you should use the shrunken LFCs as it took into account the variance of the changes. For more information, refer to this vignette to find details on moderated LFCs: https://www.bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html ...
written 20 days ago by mikhael.manurung30
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Comment: C: variancePartition - testing for individuals
... What if you include other variables as random effects (such as tumor_stage)? ...
written 20 days ago by mikhael.manurung30
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Cydar's countCells tolerance parameter for arcsinh-transformed data
... Dear all, How should I determine the tolerance setting for countCells in Cydar? The package tutorial recommended 0.5 for logicle-transformed data. Unfortunately, my data is already arcsinh-transformed so I do not think that I can still use the tutorial's recommended value. When I plot my CyTOF dat ...
cytof cydar written 21 days ago by mikhael.manurung30 • updated 20 days ago by Aaron Lun23k
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Comment: C: variancePartition - testing for individuals
... How many samples do you have for every ```submitter_id```? I suspect that the warning is caused because you have an equal number of observations and unique ```submitter_id```. ...
written 26 days ago by mikhael.manurung30

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