iPathwayGuide™ Videos
iPathwayGuide™’s powerful meta-analysis tool allows you to compare and contrast upto 5 differential experiments at the same time. With meta-analysis, you can rapidly identify several characteristics of your phenotype comparisons and drill down to pinpoint plausible biomarkers and signatures. Watch the video below to learn the nuts and bolts of iPathwayGuide™’s meta-analysis. Be sure to watch some of our webinars on the topic as well.
Advaita has teamed up with SCIEX, the leader in Data Independent Acquisition (DIA) Mass Spectrometry for the collection and analysis of proteomics-based data. Through this collaboration, users can now bring their SWATH data from the SCIEX protein expression workflow and analyze it in the context of pathways, gene ontologies, microRNAs, and diseases. The power of iPathwayGuide™ allows you to combine protein expression experiments and contrast them with other platforms including RNA-Seq, microarrays, and targeted panels. Watch the video below to see how SCIEX SWATH proteomics data was juxtaposed to mRNA data from an RNA-Seq experiment.
iPathwayGuide™ – Affy CEL file uploading
Affymetrix microarrays are one of the most widely used gene expression platforms in the industry. iPathwayGuide™ supports the most common platforms. Look at the FAQ for the latest list of supported platforms.
The resulting file from an Affymetrix microarray is commonly known as a CEL file because of the CEL extension place on the file name. To upload your CEL files, simply drag and drop the corresponding files for the condition group and the control group. iPathwayGuide™ requires at least 3 – unique files for each group. We recommend at least 4 per group in case one of the samples is rejected during QC and normalization.
Once your files are identified, click upload to begin the process. iPathwayGuide™ will upload your files, QC check them, reject and highlight any that do not pass, normalize the files, and calculate differential expression. Depending on the number of files, this process can take 2 to 5 minutes or more.
Once the QC metrics are available, iPathwayGuide™ will present the QC stats, QC Density Box Plot, and QC Density Plot. Any samples identified for removal will be highlighted in red.
Once the Normalization is complete, iPathwayGuide™ will present the Normalized Box Plots and the Normalized Density Plot. If you wish to include any of these graphs in a paper or report, you can download the graphs using the download button.
If you are satisfied, you may proceed to the Contrasts Intake page to set the number of significant differentially expressed genes along with title and description of the report.