While using the new Metaboanalyst module: MS peaks to pathways an Error of "There is something wrong with the pathway enrichment analysis” and "Duplicates were merged” is found.
Briefly, on upload of a .txt file containing m/z, p-value and t-score (attached 1.CS.txt file) and using search parameters:
Mass Accuracy (ppm):5
Analytical Mode: Positive Mode
P-value Cutoff:0.01 and
Pathway Library: Mus musculus (mouse) [BioCyc]
no error is found for one file and resulting in the mummichog_pathway_enrichment and matched compound file.
However, the same parameter does not work for another .txt file ( attached 2.CN.txt) .
We have even tried changing the P-value Cutoff and the mass accuracy to check if any set of parameters works for all the generated .txt files. However there are many .txt files for which none of the selected parameters is without Duplicates merged error .
Kindly, help understand what exactly the error of "There is something wrong with the pathway enrichment analysis" and "duplicates were merged" means and why do we get the error.
Your valuable suggestions will be of great help.
Thanking you,
Aleena
Are you using GC-MS m/z or LC-MS m/z for e MS Peaks to Pathways Module . I think the "mummichog" algorithm used in this module is only for LC-MS data. Since GC-MS adata m/z are of fragmented ion it may not work. see the reference below
http://www.metaboanalyst.ca/resources/data/tutorial7.pdf
The data is generated by LC-MS(positive ionization mode) and using the parameters : Mass Accuracy (ppm):5, Analytical Mode: Positive Mode, P-value Cutoff:0.01 and Pathway Library: Mus musculus (mouse) [BioCyc]for the shared file 1.CS.txt , the MS Peaks to Pathways module works fine. However at the same time, it does not work for another shared file 2.CN.txt. So is the case with many other generated .txt files with m/z, p-value and t-score.
Hmm, I have not used this module earlier. So not much experienced. better to get a response from the team.
Thank you Mrinal . I will certainly wait for your answers and so far we are even waiting for answers from MetaboAnalyst team.
Hi Aleena,
Did you get an answer on this? I'm experiencing the same problem with my data...
Hi Miriam,
I could not find an answer to the above problem yet. Incase you find an answer, please share it.
Thanks,
Aleena
Hi Aleena,
Of course I'll let you know. Has the MetaboAnalyst team answered yet to your email?
Thanks Miriam. No MetaboAnalyst team(http://www.metaboanalyst.ca/faces/docs/Contact.xhtml)have not answered yet.
Dear all,
Good news! The above problem of "Duplicates merged error" in Metaboanalyst new module: "MS Peaks to Pathways" no longer shows. So, the pathway analysis can be successfully performed.
Mrinal Kumar Das Miriam Popkes
Thank you...
Dear all,
I have a problem with this software each time that i want to use PLS-DA i get this page!!
please any answer
thanks
sincerely,
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