tSNE with groups of different size - reduce dataset or set perplexity = largest group?
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
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
add a comment |
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
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
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
add a comment |
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
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
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
r dimension
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
asked Nov 22 '18 at 8:11
Sebastian HesseSebastian Hesse
618
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
add a comment |
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
add a comment |
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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