diffcyt
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lmweber
R package for differential discovery analyses in high-dimensional cytometry data
Hi! thank you for this package and for the useful tutorials! I am working on CyTOF generated data, where I have four groups of treatments, and I want to make...
Hello, Could you help me with the `show_logFC` argument in the `topTable` function? When I set it equal to `TRUE`, I receive an error: Error: subscript contains invalid names I...
Fixed the calcCounts and calcMedians Functions and Added Option to Choose Which Clustering Is Used
Dear Lukas, I have fixed the `calcCounts` and `calcMedians` functions so that the rows and columns of SCEs are read properly. I have also added an option to pass an...
Please add the option to use a custom clustering stored in the column data when the input data is an SCE with cluster codes.
Hi, I'm running diffcyt via catalyst and I have some problems in setting up the design and contrast matrix. I have 144 samples divided into 4 conditions. I set up...
Dear Lukas, looking at the logFC values in my toptable results, I am confused as to how diffcyt calculates logFC values. If I use the median values, either in my...
See https://github.com/SamGG/diffcyt commits and email discussion
calcMedians() throws an uninformative error if no state markers are present
Hi, thank you for this helpful package. I raised an [issue](https://github.com/markrobinsonuzh/cytofWorkflow/issues/30) in the cytofWorkflow Github repo, because I am getting different results with diffcyt and edgeR. While I get reasonable...
Hi there, I am trying to do an analysis for two different columns of data. Column 1 is Reticulocyte count at T0 and column 2 is Reticulocyte count at T1....
