iPathwayGuide Support Page - FAQs

iPathwayGuide FAQs2018-10-06T12:16:42+00:00
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iPathwayGuide Frequently-Asked Questions

Do you have a User Guide?2018-10-13T11:04:54+00:00

Yes. Please download it here.

Open (PDF)
What kind of files can I upload?2018-10-13T11:06:51+00:00

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 proteomics data files
Select Affymetrix CEL files*

*Supported Affy CEL Files may take several minutes to upload

Human
Human Genome U133
Human Genome U133A 2.0
Human Genome U133 Plus 2.0
Human Genome U95
Human Genome U35K

Mouse
Mouse Expression Set 430
Mouse Expression Set 430 2.0
Mouse Genome 430A 2.0

Rat
Rat Expression Set 230
Rat Genome 230 2.0
Rat Genome U34

Download File (sample_generic_3_column_tab_delimited_file.txt)
I loaded a CuffDiff file but I cannot see it.2018-08-22T08:39:59+00:00

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.

How long does an analysis take?2018-08-22T08:40:42+00:00

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.

How much will it cost?2018-08-22T08:41:15+00:00

iPathwayGuide is 100% FREE to use and view for your first 3 datasets. Your first 3 reports have a 72 hour FREE preview period. To unlock download and meta-analysis capabilities, you must purchase each dataset. After the first 3 datasets, all subsequent analyses must be purchased to view, download, or be used in any meta analysis.

Creation of multiple accounts to gain a new preview period is strictly forbidden under the terms set forth by the End User License Agreement (EULA). So please don’t do that.

Reports may be purchased individually via credit card or PayPal. 30-day and Annual subscriptions are also available for purchase. Call one of our representatives today to get a customized quotation. 734-922-0110

Do you have a legend to help me read the pathway maps?2018-08-22T08:46:15+00:00

Click image for a larger view or visit KEGG.

Can I share a report?2018-08-22T08:49:40+00:00

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.

Why is the ‘Creation Time’ different from my clock?2018-08-22T08:50:16+00:00

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

What browsers do you support?2018-08-22T08:51:10+00:00

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​​
Do you have a sample files I can try?2018-10-13T11:09:13+00:00

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 (human_deseq.res.csv)
Download (human_edger_sample_tabdelimited.txt)
Download (human_jmp_genomics_sample.txt)
Download (human_nanostring_nsolver_sample_dataset.txt)
Download (human_geo2r_limma_sample.txt)
Download (human_custom_file_sample.txt)
Download (human_sciex_swath_sample.txt)
Can I change my password?2018-08-22T08:52:32+00:00

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

What databases are used in iPathwayGuide?2018-08-22T08:53:04+00:00

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?2018-10-13T11:10:14+00:00

Please refer to the following guide or the user manual.

Citing iPathway Guide

Why do I get different results with GEO2R vs. your CEL file uploader?2018-08-22T08:57:29+00:00

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.

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