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uci-cbcl / D-GEX

Deep learning for gene expression inference
GNU General Public License v2.0
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Paper Dataset #5

Closed FarshidShekari closed 5 years ago

FarshidShekari commented 5 years ago

Hi I found your dataset in this URL and I downloat thems but after download completed they extension change into .hdf files. can you help me? thanks.

yil8 commented 5 years ago

@FarshidShekari Hi, I have never seen this issue before. Can you just change back from .hdf to .gctx?

FarshidShekari commented 5 years ago

I do that but when I use cmapPy(1ktools you used in your code is deprecated) that give me error on that's file is not gctx?

yil8 commented 5 years ago

@FarshidShekari Can you copy paste the error message here?

FarshidShekari commented 5 years ago

I before fix it, but now I get memory Error when reading gctx file into gct,

yil8 commented 5 years ago

@FarshidShekari did you use exactly the v1.1 of l1ktools ? I remember they changed their API later.

FarshidShekari commented 5 years ago

No, as I said, l1ktools lib is deprecated and I use cmapPy lib as an alternative.

yil8 commented 5 years ago

@FarshidShekari sorry, I did not pay enough attention. I would still recommend using l1ktools v1.1 (https://github.com/cmap/l1ktools/releases/tag/v1.1), since I've only tested on this one. I not quite familiar with cmapPy.