Principal Component Analysis and t-SNE

[wulin teoParticipant]

Dear developers,

While I am new to DataGraph, I heavily use the available “Example file” from DataGraph to generate graphs. I could not find examples for principal component analysis and t-SNE. Can you add such examples to the template?

 

Thanks!

[gamal akabaniParticipant]

Teo,

I am all for it, but I am not sure if DataGraph does PCA or t-SNE for the moment – correct me if I am wrong. I have indicated the need for bioinformatics tools that are comparable to those found in R.

[dgteamModerator]

Correct that we do not have examples of these currently in DataGraph.  One option for now would be running the analysis in R and using the DataGraph R package to get the results in DG.

If you have any example data/scripts to conduct PCA or t-SNE in R, that would be helpful. For example, we can see how the input and output data is formatted.  If you have any example data we could use for testing please email (Help > Ask Question via email).

[wulin teoParticipant]

I use IGOR pro to run PCA analysis before I added DataGraph to my data management toolbox, so I am not an expert in R. However, I found a website that runs the PCR analysis in R using spectral data,  which is very similar to what I do.

For your reference:
https://learnche.org/pid/latent-variable-modelling/principal-component-analysis/pca-example-analysis-of-spectral-data

To analyze my spectral data, I will keep using IGOR pro for the time being. Thanks for your quick response.

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