Do you have a User Guide for iPathwayGuide™?
Yes. Please download it here. Open (PDF)
What kind of files can I upload?
iPathwayGuide™ supports analysis of Human, mouse, and rat. It supports the following files formats: CuffDiff DESeq EdgeR SAS/JMP Genomics nSolver (NanoString Technologies) Generic tab delimited .txt file (must contain gene symbol or uniprot ID, log2FC, p-value) SCIEX SWATH 2.0 [...]
I loaded a CuffDiff file but I cannot see it.
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 [...]
How long does an analysis take?
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.
Do you offer a free trial?
It is a great idea to use the software and explore the capabilities before making a purchase. The way to do this is to create a free account on our web site www.advaitabio.com. Once you create an account, you will [...]
Do you have a legend to help me read the various diagrams?
Here are the legends describing the symbols used on the pathway diagrams, gene networks and GO directed acyclic graph, respectively. Click an image for a larger view.
Can I share a report?
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. [...]
Why is the ‘Creation Time’ different from my clock?
We report the 'Creation Time' based on Coordinated Universal Time (UTC).
What browsers do you support?
iPathwayGuide™ is designed to work with all the latest major browser platforms: Google Chrome Mozilla Firefox Microsoft Edge Apple Safari (Mac only, iOS not supported yet) Microsoft Internet Explorer 11 - Some image download capabilities may not function
Do you have sample files I can try?
iPathwayGuide™ works with the most popular differential expression files. Some 3rd party emulators (e.g. Galaxy) may structure their data slightly differently. Click on the sample files below to see the structure of these files. Download Download Download Download Download [...]
Can I change my password?
Yes. From the login menu, click reset password. You will receive an email with the new password.
What databases are used in iPathwayGuide™?
A list of databases and versions is available from within each report. See our Release Notes to see the latest data.
How should I cite iPathwayGuide™?
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: - Functional analysis [Target analysis/Impact analysis/Molecular Signature analysis/Gene Ontology Term [...]
Why do I get different results with GEO2R vs. your CEL file uploader?
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™.