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theislab / destiny

R package for single cell and other data analysis using diffusion maps
https://theislab.github.io/destiny/
GNU General Public License v3.0
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Non-existent duplicate rows removed from data #47

Closed SBassler closed 3 years ago

SBassler commented 3 years ago

Hey everyone, first of all, thanks for the great package! Unfortunately, there appears to be some error with the dataset_extract_doublematrix function. It always removes some random rows which have different names in the "Cell" column, which I confirmed by running the duplicated function on it, myself ( as well as making sure length(unique(data$Cell) == length(data$Cell).

I then always get this error message: Warning message: In dataset_extract_doublematrix(data, vars) : Duplicate rows removed from data. Consider explicitly using df[!duplicated(df), ]

Interestingly, its also not related to specific samples. If I subset my patients 1:15, DiffusionMap works, 13:55 works but 12 to 55 gives the mentioned error of removed duplicated rows. It must be some kind of weird check going on in the background, which is definitely not related to duplicated rows. Many thanks and best wishes, Stefan

Sophia409 commented 2 years ago

Hi, SBassler. I came into the same question as you. How did you solve it ? @SBassler