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spficklin / RMTGeneNet

Construction of gene co-expression networks with Random Matrix Theory (RMT) thresholding.
GNU General Public License v2.0
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Tab delimited correlation matrix as input? #4

Open qichao1984 opened 8 years ago

qichao1984 commented 8 years ago

Hi Stephen, It's really exiting that you implemented RMT in C. I am a collaborator of Feng Luo and use RMT based network approach a lot. Could you please modify the code a little bit to support tab delimited correlation file as input? This would also extend the RMT approach to many different correlation methods. Thanks! Qichao Tu

spficklin commented 8 years ago

Hi Quichao,

I think the code should read in tab delimited files. I'm certain I've used them before and looking at the code it seems as though it can support them. What sort of error do you get when you try to use a tab delimited file?

qichao1984 commented 8 years ago

Hi Stephen,

I received a "Segmentation fault (core dumped)" regardless the matrix size in the file. And I read the instruction and seemed it takes .bin file as input. The file format looks like below: OTUID 1 2 3 4 5 1 1 0.1 0.2 0.3 0.4 2 0.1 1 0.2 0.3 0.4 3................. 4................. 5................ Any ideas? Thanks!

Qichao

On Thu, Apr 14, 2016 at 12:13 PM, Stephen Ficklin notifications@github.com wrote:

Hi Quichao,

I think the code should read in tab delimited files. I'm certain I've used them before and looking at the code it seems as though it can support them. What sort of error do you get when you try to use a tab delimited file?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/spficklin/RMTGeneNet/issues/4#issuecomment-209753565

spficklin commented 8 years ago

Is this line the header:

OTUID 1 2 3 4 5

If so, try removing the OTUID. The header should only contain the sample names.

qichao1984 commented 8 years ago

Still not working...Do you have an example file for me to try? Thanks!

On Thu, Apr 14, 2016 at 12:34 PM, Stephen Ficklin notifications@github.com wrote:

Is this line the header:

OTUID 1 2 3 4 5

If so, try removing the OTUID. The header should only contain the sample names.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/spficklin/RMTGeneNet/issues/4#issuecomment-209758113

spficklin commented 8 years ago

There is an example directory with a sample yeast expression matrix that you can try. Although it has no headers. If you replace spaces with tabs you can test it as tab-delimited.

spficklin commented 8 years ago

Oh, and the README has instructions for how to test the example.

qichao1984 commented 8 years ago

Oops, maybe we are having misunderstandings. I'm asking about letting rmm command (the random matrix modeling) to support tab delimited correlation file as input, instead of binary files. This would be very helpful when using correlation matrix generated by other methods, not the ccm command.

On Thu, Apr 14, 2016 at 1:10 PM, Stephen Ficklin notifications@github.com wrote:

Oh, and the README has instructions for how to test the example.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/spficklin/RMTGeneNet/issues/4#issuecomment-209764477

spficklin commented 8 years ago

Oh I see. Yes, you specified 'correlation files' in your original post but I misunderstood. Apologies. The software currently only supports the binary format for RMT thresholding. We are working on an updated version of this software which will be released as a separate project. It's still a bit away from being released but we can add add it to our TODO list to try to support import of tab-delimited correlation files.

qichao1984 commented 8 years ago

Sounds nice! Looking forward to your new version!

On Thu, Apr 14, 2016 at 2:02 PM, Stephen Ficklin notifications@github.com wrote:

Oh I see. Yes, you specified 'correlation files' in your original post but I misunderstood. Apologies. The software currently only supports the binary format for RMT thresholding. We are working on an updated version of this software which will be released as a separate project. It's still a bit away from being released but we can add add it to our TODO list to try to support import of tab-delimited correlation files.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/spficklin/RMTGeneNet/issues/4#issuecomment-209775459

youzi07 commented 7 years ago

Hi Stephen, I'm very interested in your implemented RMT. And I'm also looking forward to your new version that 'correlation files' as input.