integrate multi-omics data sets
This is a demo of integrating transcriptomics, proteomics and metabolomics data sets to view on a pathway together on Subio Platform.
There are 2 ways.- Keep original IDs and integrate in the merged platform.
- Discard original IDs and integrate in a new platform of common IDs.
Option 1 is also used to merge data of multiple arrays like GeneChipA and ChipB. And option 2 is applicable to integrate different microarray platforms to compare like Affymetrix, Agilent and RNA-Seq data.
Option 1: Keep original IDs and integrate in the merged platform.
00:00 Viewing the 3 types of data sets.
00:30 Exporting SSA files of the 3 series, and import back them.
01:40 Merging the 3 platforms of different omics data.
02:20 Creating a series of all the samples of different omics.
03:05 Setting up "All Samples"and "Merged" DataSets.
03:20 Applying normalization and turning into log ratio against control in each omics data set.
03:50 Browsing DataSets to see the difference.
04:10 Editing the annotation table.
05:15 Creating Measurement Lists for each omics data.
06:30 Importing a pathway data.
06:50 Browsing the different omics data on a pathway together.
Option 2: Discard original IDs and integrate in a new platform of common IDs.
07:10 Checking that both transcriptomics and proteomics data have common ID (Gene Symbol in this case).
07:30 Exporting the table of log ratios against control in transcriptomics.
07:45 Exporting the table of log ratios of proteomics.
08:05 Importing the log ratio table of transcriptomics as creating a new platform of the set of Gene Symbols.
08:45 Importing the log ratio table of proteomics into the newly created platform.
09:55 Creating a new series of the samples from different 2 omics.
10:20 Applying only "Import Log Ratio" normalization block.
10:30 Setting up DataSets of "All Samples," "transcriptomics" and "proteomics" respectively.
11:00 Importing a pathway data.
11:25 Browsing patterns of transcriptomics and proteomics on a pathway at the same time.
Please take an Online Training for a full instruction of the data analysis.
Maybe it's a little bit tricky. Please request online support so that we guide your operation. Or please consider purchasing Analysis Service to let us do it for you.