Search Types

From Array Suite Wiki

The Search server for dropdown box contains 8 different searches that can be performed with Array Server:

Image371.png

Project list: searches the server for a list of projects meeting the criteria specified by the search options. This is most useful for quickly finding projects for further analysis, visualization, and exporting.

Ranked Variable List: searches the server for a scored list of genes best representing the searched projects. This could be useful to get a ranked list of genes corresponding to a disease area, for example. It uses a scoring system that bins the p-value rank scores into three categories, and then uses a composite score of those scores to come up with the top genes for that list of projects. The results table shows the total score, as well as the binned scores for both up and down direction. Clicking on a gene in the report will show the ranked project list with variable profiles (explained below) for that gene and subset of projects.

Inference reports (fold changes, p-values, etc.): searches the server for any inference reports matching a set criteria. An Inference Report contains one or more comparisons that were calculated on the server, each containing a set of p-values, fold changes, etc. This search provides a nice way to look at data across projects, as fold changes can be directly comparable without worrying about normalization issues. More information on the results of the search can be found by clicking this link: Search Inference Report.

Ranked project list with variable profiles: searches the server for a ranked list of contrasts matching a set criteria for a single variable (gene). Each contrast/project is scored using the rank of the p-value for that variable in its contrast. High scores indicate that the variable is one of the top p-values for that contrast and can give you an idea of how important this variable is in that project/contrast. From there, the user can further investigate the data. More information on the results of the search can be found by clicking this link: Ranked Project List

Detailed variable data: searches the server for a single variable matching a set criteria, and returns all of the information on the server for that particular variable (i.e. fold change, LSMean, p-value, etc.). The user can further investigate the individual data from that point. More information the results of the search can be found by clicking this link: Search Variable Data.

Raw observation data: searches the server for one or more variables matching a set of criteria, and returns the primary data for that observation. This is a way to look at data across multiple projects. Omicsoft provides a method of median normalization that can be used to attempt to visualize data from a wide range of datasets and make them comparable (normally this would not be ideal as there are a number of factors which can influence a dataset, including the normalization done to the dataset). More information on the results of this search can be found by clicking this link: Search Observation Data.

Observation data adjusted by controls: searches the server in a manner similar to search observation data, for one or more variables matching a set of criteria, and returns the data, adjusted by controls. This provides the best method for comparing expression levels across projects/samples, as it allows the user to look at individual data points, adjusted by the mean/median of its control. This requires that special properties be set for a dataset to indicate which comparisons should be made. This is automatically done for all Omicsoft-processed GEO data as well as any user-based pipeline projects. More information on the results of this search can be found by clicking this link: Search Observation data adjusted by controls.

CNV segments: searches the server for any CNV segment matching a set criteria. Most often the user will use advanced options to specify which chromosome, or chromosome region, to search (rather than searching for a single variable). More information on the results of this search can be found by clicking this link: Search CNV Segment.