Always get an error about version when using this in SEURAT 3.1.5

[MeganQiu]

Dear developer,

I am using this method in Seurat 3.1.5 in windows 10. I extracted the libfftw3-3.dll and FIt-SNE.exe in bin/ folder and included the following commands in my code:

source("D:/FIt-SNE-1.2.1/fast_tsne.R", chdir=T)
tsne = RunTSNE(clustered.tumor, dims = 1:75, tsne.method = "FIt-SNE", nthreads = 4, max_iter = 2000, 
               fast_tsne_path="D:/FIt-SNE-1.2.1/bin/FItSNE.exe")

However, when running the above codes, I got the following errors:

> source("D:/FIt-SNE-1.2.1/fast_tsne.R", chdir=T) FIt-SNE R wrapper loading. FIt-SNE root directory was set to D:/FIt-SNE-1.2.1

> tsne = RunTSNE(cluster.tumor, dims = 1:75, tsne.method = "FIt-SNE", nthreads = 4, max_iter = 2000, 
+                fast_tsne_path="D:/FIt-SNE-1.2.1/bin/FItSNE.exe")

Warning: The following arguments are not used: pca First line of fast_tsne output is =============== t-SNE v1.2.1 =============== Error in fftRtsne(X = object, dims = dim.embed, rand_seed = seed.use, : Our FIt-SNE wrapper requires FIt-SNE v1.X.X, please install the appropriate version from github.com/KlugerLab/FIt-SNE and have fast_tsne_path point to it if it's not in your path

As you can see, I am using the newest version of FIt-SNE, but still get an error related to version issues. Do you have any ideas about this error?

By the way, I also tried to compile it on Mac, but got the same error as the above one. Thank you in advance for you help.

Best regards, Megan

[dkobak]

This means that the Seurat wrapper should be updated. Indeed, it does not support Fit-SNE 1.2: https://github.com/satijalab/seurat/blob/b51801bc4b1a66aed5456473c9fe0be884994c93/R/dimensional_reduction.R#L1820

Until this is fixed, you could install FIt-SNE 1.1 instead of 1.2.

[MeganQiu]

Solved! Thank you so much!

[dkobak]

I reopen this though, because it should be fixed in Seurat. Hopefully @linqiaozhi can take care of that.