GEO dataset get C2 subtype only

[kodayu]

Hi,

This is a great package that can help our research a lot, even though a little bit difficult to install. However, these are not the emphasis.

I have used this package for several datasets classification, however, I found that only in TCGA datasets, it can perform well. for several GEO dataset (I have tried 7 sets, all are microarray), I can get C2 subtype only.

Then I tried a TARGET dataset, which is sequenced by RNA-seq. I can get C1, C4 and only a few C6/C2 subtypes. I don't know why? Maybe this dataset do have only a few C6/C2 subtypes.

So, I wonder whether this package can not be used for microarray data? but it's built by pearson correlation analysis, I do not think microarray data is not applicable.

sincerely yours!

[Gibbsdavidl]

Hi thanks for writing!
I appreciate the feedback and I'll try to make it easier to install.

I am not sure about whether it's suitable for microarray. The best test, would be to find some data where samples were run on RNA-seq and microarray as a comparison... then we could compare the subtype calls.

Yeah, whenever running new data, it's very hard to know what to expect. There's no ground truth unfortunately.

The classifier is now loosely based on 'Top Scoring Pairs" classification. There's no correlations being computed, but rather (mostly) binary features comparing pairs of genes. (if gene_1 > gene_2 then 1 else 0).

I would think microarray would work, but I haven't confirmed it.

Thanks!
-dave