In omics data analysis, it is sometimes assumed that advanced statistical plug-ins are required in order to obtain meaningful results. However, the essence of data analysis is not to search for answers inside the “black box” of an algorithm.
Even with the core features of Subio Platform, you can capture many aspects of the data’s condition and detect potential irregularities. In fact, before running statistical procedures, interacting with the data through your own eyes is one of the most important steps that determines the quality of the analysis.
1. Look at the raw state of your data before normalization and preprocessing
In many analysis workflows, data are normalized immediately after import, and the process quickly moves on to statistical analysis or lists of P-values. However, before normalization, it is extremely important to understand what state the data are actually in.
With Subio Platform, you can examine experimental parameters and expression data distributions using histograms and other viewers as you proceed with the analysis. This allows you to visually recognize data bias and differences between samples before computational processing begins.
In addition, normalization and preprocessing can also be examined within the free version of Subio Platform. Even without plug-ins, you can try different normalization methods, adjust filtering conditions, check the state of the data, and consider the appropriate direction for your analysis.
For example, are only the samples from a particular condition or processing date showing shifted distributions, unrelated to biological differences? In samples with extremely low read counts, is noise being amplified after normalization? These issues are not always solved automatically, no matter how sophisticated the algorithm may be.
That is why it is important to check the state of the data with your own eyes before moving on to statistical analysis. With Subio Platform, this kind of examination and trial-and-error process can begin with the free core features alone.
2. Do not let plug-in analysis end as a one-time result
Subio Platform plug-ins are priced to make advanced computational methods easy to introduce and accessible to many users. However, the value of plug-ins is not limited to running calculations.
In Subio Platform, analysis results generated using plug-ins are also saved
within the free Subio Platform environment.
Therefore, even after the plug-in license period has ended,
you can continue to access not only the data itself,
but also the analysis results obtained using the plug-ins.
In many commercial analysis software environments,
it may be difficult to sufficiently review past analysis results after a license has expired.
In contrast, Subio Platform allows analysis results to remain available
in a form that can be reviewed later.
When needed, you can also activate the plug-in again and easily perform additional analyses based on the saved data and analysis results. This means that analysis results do not have to end as one-time output files. Instead, when new ideas or biological insights arise, past analysis results can be re-examined, discussed, and shared as research assets.
3. Use a free environment for the trial-and-error process that takes the most time in analysis
When preparing final data for a paper or conference presentation, there are certainly situations where statistical plug-ins are needed. However, in actual analysis work, the time spent without plug-ins is often longer. This is because real data analysis is not a one-way process like the workflow described in a paper. It is a continuous process of trial and error.
You may repeatedly change normalization or preprocessing conditions, view the data from multiple angles using different viewers, search for genes of interest by keyword or through web searches, or combine multiple conditions using Venn diagrams. These processes, which are central to data analysis, can all be carried out using the free core features of Subio Platform. We believe that the thinking process, where analysts spend the most time, should be as free and flexible as possible.
4. Check your data immediately, wherever an idea comes to you
Because Subio Platform can be used free of charge, it can be installed on multiple computers in a laboratory, and copies of the data can be kept where they are needed. This means more than simply reducing cost.
Ideas that suddenly come to mind should be tested before their momentum fades. You do not need to be restricted by license limitations or wait until you can access a specific licensed computer. At your desk, in a corner of the laboratory, or wherever the idea arises, you can immediately check the data. Creating an environment where your thinking does not stop, without adding cost, is one of the major values Subio Platform provides.
5. Share “living data” to maximize the intelligence of your team
Analysis is not something that has to be completed by one person alone. With Subio Platform, analysis results can be shared within a team not merely as static figures, but as interactive “living data”. Using powerful viewers, each team member can examine the data from their own perspective, review the analysis process, and compare results if needed.
Not every member of the research team needs to have paid plug-ins. A team member with analysis experience can perform the core analysis using plug-ins and share the project file. Other members can then use the free Subio Platform on their own computers to explore the data more deeply and develop discussions. This environment where everyone can interact with the data greatly expands the opportunities for new discoveries.
6. Data Analysis Service: specialists support your project as part of your team
If your laboratory does not have members with sufficient analysis experience, please consider using Subio’s Data Analysis Service.