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.