The Vector Inspector allows you to apply the same dimensionality reduction parameters (DRPs) to new samples, to see the weight of parameters comprising DRPs, and to export those parameters as gene sets.
DRPs such as LDA or PCA are new combinations of parameters whose contribution is weighted differently. The combined amount or “weight” of these parameters contributed to any DRP is called a vector. The Vector Inspector feature in SeqGeq allows a researcher to see which parameters contribute most to any DRP calculated within the platform. This extra set of information is stored in SeqGeq as a “Derived Observation of Genes”.
Often times researchers will concatenate samples together in order to created DRPs which apply to all events within a given data set. However, for some analyses this may not be possible or desirable, in which case the Vector Inspector can be used to apply DRPs calculated for one sample to others.
Using the Vector Inspector
To access the tool you will first need to have already calculated DRPs for a given sample, using the Dimensionality Reduction platform. You’ll then select a sample, and click the Vector Inspector button within the Discovery ribbon of SeqGeq’s workspace:
Within the Vector Inspector window that pops up, selecting a Vector Set will allow you to view all of the vectors associated with DRPs calculated for the data selected. Selecting one of the vectors will illustrate weights (aka “Relative Importance”) associated with each parameter within the chosen DRP Vector. Selecting multiple vectors will sum the absolute values of parameter’s weights within those chosen vectors:
Within the vector(s) chosen you can create a gene set from the genes illustrated there, by first selecting them, and then clicking “Convert to a Gene Set”:
If you have acquired a new set of data you can apply the vectors calculated on another set, in order to make these DRPs comparable, by adding the new data set to your workspace, selecting one of those new files, and accessing the Vector Inspector. From this dialog you can select the vector set and associated vectors you’d like applied to the new data, and click the button “Calculate Derived Parameters”:
This will copy the previously calculated vectors into your new data file:
If you have questions about this feature, or any of the other tools in SeqGeq please reach out to our team of applications engineers: firstname.lastname@example.org