Please make sure your are using the “…gene_exp.diff” file that comes from CuffLinks. There are some applications that claim to emulate CuffDiff output (e.g. Galaxy). If you are using one of these applications, please make sure the output file has all columns populated. See below for specific columns that must be present. Also, use this link to view the Cuffdiff manual.

Generally, each analysis takes about 15 minutes to complete. If there are other analyses queued ahead of yours, it may take a bit longer. You will receive an email as soon as the analysis is complete.

Yes, there are a few ways that you can experience all of the functionalities of iPathwayGuide. We provide several demo analyses that are automatically shared when you register for a free account. These datasets cover a range of experiment types, conditions, and analysis outcomes. You have full access to interact with all of the demo analyses and experience all of the features of iPathwayGuide. We also provide sample data files, which allows you to try out the data intake process before uploading your own data.

You can analyze a complete experiment for only $149. This will provide a full interactive report that you can use to further explore your results in many ways, including discovering mechanisms. The interactive report can be shared with others at no additional cost. The price also includes a PDF report that many of our users use as the Methods or Supplementary Materials in their published peer-reviewed articles. This automatically-generated PDF contains a full description of your input data, experiment, methods, results with figures, and references.

Yes! From the dashboard, just click share on any completed report. Then enter the email address for the person you wish to share it with. If they do not have an account, they will be prompted to create on. Once registered, they will be able to view the report.

We report the ‘Creation Time’ based on Coordinated Universal Time (UTC).

iPathwayGuide is designed to work with all the latest major browser platforms:

• Google Chrome
• Mozilla Firefox
• Apple Safari (Mac only, iOS not supported yet)
• Microsoft Internet Explorer 11 – Some image download capabilities may not function​​

Yes. From the login menu, click reset password. You will receive an email with the new password.

A list of databases and versions is available from within each report. See our Release Notes to see the latest data.

Citing iPathwayGuide

Using Advaita Bio’s products or content for any form of publication (e.g. print, electronically) requires researchers to cite them. Please use one of the options below for citations:

• “The Data (significantly impacted pathways, biological processes, molecular interactions, miRNAs, SNPs, etc.) were analyzed using Advaita Bio’s iPathwayGuide (https://www.advaitabio.com/ipathwayguide).”

• “This software analysis tool implements the ‘Impact Analysis’ 1 approach that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc., as described in (Draghici, 2007, Donato, 2013).”

¹Sorin Draghici, Purvesh Khatri, Adi Laurentiu Tarca, Kashyap Amin, Arina Done, Calin Voichita, Constantin Georgescu, and Roberto Romero. A systems biology approach for pathway level analysis. Genome Research, 17:1537-1545, 2007.

• LaTeX users may use the following code in the bibtex file:

~\cite{advaita2014}

@ONLINE{advaita2014,
author = {Advaita, Corporation},
title = {Pathway Analysis with iPathwayGuide},
month = Jun,
year = {2014},
url = {https://advaitabio.com/ipathwayguide}
}

For additional guidance, please contact info@advaitacorporation.com.

GEO2R does not perform normalization for Affymetrix CEL files. The Advaita iPathwayGuide CEL file uploader currently utilizes the Gene-chip Robust Multi-array Average (GCRMA) normalization method. As such, there can be discrepancies between CEL files processed with GEO2R vs. iPathwayGuide.