Tab delimited correlation matrix as input?

[qichao1984]

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]

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]

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 [email protected]
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?

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#4 (comment)

[spficklin]

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]

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 [email protected]
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.

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#4 (comment)

[spficklin]

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]

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

[qichao1984]

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 [email protected]
wrote:

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

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[spficklin]

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]

Sounds nice! Looking forward to your new version!

On Thu, Apr 14, 2016 at 2:02 PM, Stephen Ficklin [email protected]
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.

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#4 (comment)

[youzi07]

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.