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naikai / sake

sake
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8 nodes produced errors; first error: Remove duplicates before running TSNE #9

Closed naikai closed 8 years ago

naikai commented 8 years ago

Some files will generate this kind of problems, such as the ALS file Wen-wei provided

Maybe add a step to check (and remove) duplicated rownames?

naikai commented 8 years ago

Added a step to check for perplexity before running t-SNE.

In default Rtsne package, they require: perplexity * 3 < (ncol(x) - 1)

naikai commented 8 years ago

Add checking for duplicated columns in the data Rows (genes) may have same expression values? (most likely to be those lowly expressed genes)