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Significance Analysis of Interactome: probabilistic filtering of quantitative AP-MS data.

Project Members:

• Guo Ci Teo (admin)
• Hyungwon Choi (admin)

[Sudhir Jadhao]

Dear Guo and Hyungwon,

Greetings for the day!!

I want to analyes RIME data with saintq v4. I have downloaded the exe file and tried to run it.

But I am not able install the exe file , aftter double clicking on exe file just balck window opens and get close immediately in 2 to 3 secs.

Can you please help to solve above issue.

[Hyungwon Choi]

Hi Sudhir,

The file must be run from a command prompt (not a click-based program). To do this, you have to create an input parameter file placed in the same directory as the input data (spread sheet) according to the manuals and examples provided in the other zip file (saintq v0.0.4.tar.gz).

If you aren't familiar with using the command line interface, then you can run the other versions of SAINT (SAINTexpress) in the CRAPome website or through ProHitz. Hope you can get it to work.

Hw

[Sudhir Jadhao]

Thank you for your valuable time, I will try through CRAOome and Prohitz.

[SASI MANNE]

Hi Guo and Hyungwon,

I am trying to run saintq and getting the following error "St12out_of_range vector" and created a bug " #8 Out of range error",can you please look in to this and help me with the format of my param file and input files.

Thank you
Sasi

[SASI MANNE]

Hi,

I am trying to run saintq on Linux and am getting this error St12out_of_range vector::_M_range_check: __n (which is 2) >= this->size() (which is 1)

I swtiched operating systems from mac to linux to see if it makes any changes in error i am getting on the same dataset.

Can you check this error and see what i am doing wrong ?

Thank you
Sasi

[Estefany Guzman]

Parsing prey file prey.dat ...libc++abi.dylib: terminating with uncaught exception of type std::runtime_error: invalid delimiter

^ I am getting this error even when utilizing the prey.dat file that came with the package. Any suggestions on how to correct the issue?

[Joan Josep Bech-Serra]

Hi Guo and Hyungwon,

I am trying to improve my results in SAINT by adding interaction data in my analysis. However, I have some things that I need to clarify. In the example provided in the manual of SAINT you show a file with two columns: the first one with a list of GOIDs (not used by the software to compute the TopoAvgP) and the second one, the important one, with a list of genes separated with a blank space, for each GOID. I supose that the genes shown for each GOID (for example, for GO:0000002 you show the genes SLC25A4, TYMP, MEF2A, MPV17 and LONP1) are just the genes that are cataloged with this GOID in the gene ontology website, no matter if they really interact or not. Is this correct? I have read the paper were you show this improvement and, to me, is some how difficult to understand how this list can improve an indirect interactor with low score if the list is performed not according to already known interaction data.

Could you help me on this?

Thank you!