tSNE with groups of different size - reduce dataset or set perplexity = largest group?












1















Plotting a proteome dataset with tSNE I encounter the problem that I have a large healthy group (70) and rather few samples per genotype group (3-8).
How should I set the perplexity in this case?
Or would it better to separate the healthy cases form the diseased ones (they are clearly separated in PCA, euclidean dist ect)?



Thanks a lot!
Sebastian



Side quest: would you use batch-corrected or rather uncorrected data for the visualisation? For PCA the corrected ones look much better but I wonder if using it in tSNE would be overfitting?










share|improve this question


















  • 2





    If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

    – missuse
    Nov 22 '18 at 8:15
















1















Plotting a proteome dataset with tSNE I encounter the problem that I have a large healthy group (70) and rather few samples per genotype group (3-8).
How should I set the perplexity in this case?
Or would it better to separate the healthy cases form the diseased ones (they are clearly separated in PCA, euclidean dist ect)?



Thanks a lot!
Sebastian



Side quest: would you use batch-corrected or rather uncorrected data for the visualisation? For PCA the corrected ones look much better but I wonder if using it in tSNE would be overfitting?










share|improve this question


















  • 2





    If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

    – missuse
    Nov 22 '18 at 8:15














1












1








1








Plotting a proteome dataset with tSNE I encounter the problem that I have a large healthy group (70) and rather few samples per genotype group (3-8).
How should I set the perplexity in this case?
Or would it better to separate the healthy cases form the diseased ones (they are clearly separated in PCA, euclidean dist ect)?



Thanks a lot!
Sebastian



Side quest: would you use batch-corrected or rather uncorrected data for the visualisation? For PCA the corrected ones look much better but I wonder if using it in tSNE would be overfitting?










share|improve this question














Plotting a proteome dataset with tSNE I encounter the problem that I have a large healthy group (70) and rather few samples per genotype group (3-8).
How should I set the perplexity in this case?
Or would it better to separate the healthy cases form the diseased ones (they are clearly separated in PCA, euclidean dist ect)?



Thanks a lot!
Sebastian



Side quest: would you use batch-corrected or rather uncorrected data for the visualisation? For PCA the corrected ones look much better but I wonder if using it in tSNE would be overfitting?







r dimension






share|improve this question













share|improve this question











share|improve this question




share|improve this question










asked Nov 22 '18 at 8:11









Sebastian HesseSebastian Hesse

618




618








  • 2





    If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

    – missuse
    Nov 22 '18 at 8:15














  • 2





    If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

    – missuse
    Nov 22 '18 at 8:15








2




2





If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

– missuse
Nov 22 '18 at 8:15





If pca looks good i wouldn't bother with t-sne. Btw this is more suited for crossvalidated.

– missuse
Nov 22 '18 at 8:15












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