loading experimental data

[nsl]

Hi,

This seems like a nice tool but can't seem to get past step 1. My data/experiment does not appear in the Node Table. I changed the Gene ID to be uniform  (Flybase gene ID) after reading some of the archived posts. Can anyone help? Any insight would be much appreciated. 

The only criteria I changed are the following

 5) Select background definition -set all 

10) Seed enrichment- # of permutations -100

Thank you.

nsl

[ucsf egan]

Hello,

Thanks for posting.  Can you post a couple of the Flybase gene IDs that you are using?  I'd like to confirm that they match the Flybase mapping file.

I'm not sure that the SEED enrichment settings are causing the problem, but I'd like to advise you:

1) SEED enrichment should be done only if you have loaded all stats/p-values for all genes from your experiment - not just the most significant.

2) The background for SEED should be relative to your experiment - the "first" option, will work, as that sets the background to all genes in the first experiment file you define.

Thanks!

Jesse

[nadisha silva]

Hi Jesse,

Thank you for getting back to me. Here are the first couple of rows from my input file. Gene ID, Fold change & P val .

FBGN0031216 -1.40048 4.95E-05

FBGN0260749 -0.558758 0.00117942

FBGN0259750 -4.1667 3.66E-05

FBGN0040232 -1.03696 0.00246345

FBGN0031307 -4.60682 0.00016402

FBGN0003313 -2.79351 0.000127198

FBGN0032363 -1.02459 0.000692729

FBGN0025683 -0.661466 0.00145214

FBGN0032456 -0.997759 3.20E-08

Sincerely,

Nadisha

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[ucsf egan]

Just to follow up, this issue was resolved by using a custom mapping file that contained FlyBase IDs in all caps.

jesse