T-Statistic Stochastic Neighbour Embedding In R For Grouping Gene Expression Data
0
0
Entering edit mode
12.0 years ago
Diana ▴ 910

Hello everyone,

I am analysing gene expression data which is normalized. I've clustered it using different techniques such as hierarchical and k-means and I've recently attempted to group it using t-SNE so I can see how different techniques would group the genes according to their expression patterns across our experiment. When I try to use the package tsne in R, its as follows. First I created a distance matrix for the data using dist() and then I'm using tsne function:

t = tsne(distance_matrix, initial_config = NULL, k = 2, initial_dims = 30, perplexity = 30, max_iter = 1000, min_cost = 0, epoch_callback = NULL, whiten = TRUE, epoch=100)

I get the following error which I don't understand:

sigma summary: Min. : 0.05865 |1st Qu. : 0.07213 |Median : 0.07861 |Mean : 0.08058 |3rd Qu. : 0.09074 |Max. : 0.1056 |
Epoch: Iteration #100 error is: 12.3600149047312
Epoch: Iteration #200 error is: 0.782907087502658
Epoch: Iteration #300 error is: 0.482898016719146

tsne package: http://cran.r-project.org/web/packages/tsne/tsne.pdf

Please help! Many thanks.

r gene-expression • 7.3k views
ADD COMMENT
0
Entering edit mode

Are you sure you're getting an error? It looks as if tsne is just being verbose and just letting you know about the "state of affairs" after every 100 iterations. Is there something in your t variable? Also, you should pick another variable besides t so as to not avoid the confusion between your var and the transpose function.

ADD REPLY
0
Entering edit mode

Thank you. I changed the variable name and I'm still getting the same. If it is telling me something, there's no documentation for it in the manual and I cant really figure out what this means and if it's something important.

ADD REPLY
0
Entering edit mode

What I'm saying is that if the "result" you are getting is only the part you pasted in, then it doesn't look like this is an error. It looks as if the tsne function is only printing to "stdout" telling you about the progress that it is making after every 100 iterations.

After you run tsne, does it return something to you? If you run x <- tsne(...), what does is(x) give you?

ADD REPLY
0
Entering edit mode

It gives me this : [1] "matrix" "array" "structure" "vector"

ADD REPLY
0
Entering edit mode

Great -- so ... we're done, right? To recap: tsne is not failing with an error, and you get what you want. The "verbosity" after you call tsne is just keeping you "up to speed" with what the function is doing internally while it is running.

ADD REPLY
0
Entering edit mode

Thanks a lot Steve!!

ADD REPLY

Login before adding your answer.

Traffic: 2854 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6