iPathwayGuide FAQs2018-10-30T12:26:34-04:00
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iPathwayGuide Frequently-Asked Questions

I went back to analyses that I had previously paid for, opened them and a warning came up for indicated that the analyses were “deprecated” so I hit the re-analyze button only to find that the files are now locked and require payment to open. What is going on and how do I access the analysis I already paid for?2019-07-08T07:58:15-04:00
We periodically update our knowledge base with the latest annotations and references. This  is necessary in order to offer our users an analysis that uses the most recent knowledge available. This in fact, is one of the main value points that we provide to our users. Just to give you an idea, the sheer data available now is approximatively 4 times larger than what we had 18 months ago. Furthermore, brand new analysis capabilities are added all the time. For instance, during the past year alone we added an extremely powerful network analysis which is able to discover new mechanisms, as well as a very sophisticated upstream regulator analysis. If you have not seen these yet, it would be worth your time to schedule a 30 min phone call for us to show these to you.
When new knowledge becomes available, our platform lets you know by marking your existing analyses as “deprecated”. Thus, you are aware that they are not based on the latest knowledge available in the field. It is better to find this out from us, rather than from the reviewers of your grant or paper pointing out that your analysis does not mention such and such recent discovery. You original analysis is still fully available to you. You can simply close the warning messages at the top by clicking the X symbol at the top left, immediately to the left of the analysis title. Every single piece of information will still be there, as you saw it when the analysis was first performed.
When new knowledge becomes available, you may or may not choose to analyze the data again, using the latest knowledge available. If you choose do resubmit the data for a new analysis and you have a valid subscription, this additional analysis will incur no additional cost. However, if your subscription has expired, you will need to either renew it or pay for the individual analyses that you wish to have done. Please keep in mind that updating an existing analysis involves a resubmission of the original data and a complete re-analysis of that data from scratch. For each analysis, we ourselves are incurring all the costs associated to the computation and the storage on the AWS platform.
Here is a blog comparing the single analysis vs. subscription usage: https://advaitabio.com/ipathwayguide/subscription-vs-purchasing-individual-analyses-which-one-do-i-want/
Do you have a User Guide?2019-08-30T16:34:21-04:00

Yes. Please download it here.

Open (PDF)
What kind of files can I upload?2018-10-13T11:06:51-04:00

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.2019-01-10T19:41:19-04:00

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. Also, use this link to view the Cuffdiff manual.

Column number Column name Example Description
1 Tested id XLOC_000001 A unique identifier describing the transcipt, gene, primary transcript, or CDS being tested
2 gene Lypla1 The gene_name(s) or gene_id(s) being tested
3 locus chr1:4797771-4835363 Genomic coordinates for easy browsing to the genes or transcripts being tested.
4 sample 1 Liver Label (or number if no labels provided) of the first sample being tested
5 sample 2 Brain Label (or number if no labels provided) of the second sample being tested
6 Test status NOTEST Can be one of OK (test successful), NOTEST (not enough alignments for testing), LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL, when an ill-conditioned covariance matrix or other numerical exception prevents testing.
7 FPKMx 8.01089 FPKM of the gene in sample x
8 FPKMy 8.551545 FPKM of the gene in sample y
9 log2(FPKMy/FPKMx) 0.06531 The (base 2) log of the fold change y/x
10 test stat 0.860902 The value of the test statistic used to compute significance of the observed change in FPKM
11 p value 0.389292 The uncorrected p-value of the test statistic
12 q value 0.985216 The FDR-adjusted p-value of the test statistic
13 significant no Can be either “yes” or “no”, depending on whether p is greater then the FDR after Benjamini-Hochberg correction for multiple-testing
How long does an analysis take?2018-08-22T08:40:42-04:00

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.

Do you offer a free trial?2019-06-13T11:26:55-04:00

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 have full access to several analysis results. These datasets cover a range of experiment types, conditions, and analysis outcomes. You will be able to fully use the software to explore these data sets in whichever way you choose. You will 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 will show you some of the formats that can be used to upload data for analysis.  An alternative would be to setup a time and let one of us to show you around the software. You will learn more in a much shorter time, and you will also be able to get immediate answers to any questions you may have.

Once you get oriented with the software, if  you want to see an analysis of your own data, we offer the possibility of purchasing a single analysis. We need to charge for this because we use a backend cloud platform that costs us money for every analysis done. The price of a single analysis is meant to cover these costs. The price of the single analysis is USD 287, as of June 15th, 2019. Please see more details at https://advaitabio.com/blog/. A single analysis can be purchased with PayPal by clicking the Purchase button next to it.
Any analysis provides 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.
Once you see the capabilities of iPathwayGuide in action, we strongly suggest that you get a subscription rather than continue to purchase one analysis at a time. We will gladly refund the price of any single analyses done in the 30 days prior to ordering a subscription.  See the blog discussing single analysis vs. subscriptions at:
https://advaitabio.com/ipathwayguide/subscription-vs-purchasing-individual-analyses-which-one-do-i-want/.
Do you have a legend to help me read the various diagrams?2019-06-18T17:10:41-04:00

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.

Legend for gene networksRelationship types in GO
Can I share a report?2018-08-22T08:49:40-04:00

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?2018-08-22T08:50:16-04:00

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

What browsers do you support?2018-08-22T08:51:10-04:00

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?2018-10-13T11:09:13-04:00

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?2018-08-22T08:52:32-04:00

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

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

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?2019-07-08T08:32:11-04:00

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’ 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, Tarca, 2008, Donato, 2013, Ahsan 2018).”

A systems biology approach for pathway level analysis

S Draghici, P Khatri, AL Tarca, K Amin, A Done, C Voichita, C Georgescu, …
Genome research 17 (10), 1537-1545

Analysis and correction of crosstalk effects in pathway analysis

M Donato, Z Xu, A Tomoiaga, JG Granneman, RG MacKenzie, R Bao, …
Genome research 23 (11), 1885-1893

A novel signaling pathway impact analysis

AL Tarca, S Draghici, P Khatri, SS Hassan, P Mittal, J Kim, CJ Kim, …
Bioinformatics 25 (1), 75-8
Identifying significantly impacted pathways and putative mechanisms with iPathwayGuide

S Ahsan, S Drăghici
Current protocols in bioinformatics 57 (1), 7.15. 1-7.15. 30
If you need more explanations on how the method works or if you ever get any questions from the reviewers about the analysis, we will be happy to help preparing the response to reviewers.
Why do I get different results with GEO2R vs. your CEL file uploader?2018-08-22T08:57:29-04:00

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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