I want to run the experiments in mentioned in enter the matrix.

For the the plot in figure 3B it mentioned that

The relative absolute value of the magnitude of each element in the pattern matrix indicates the extent to which that sample contributes to the corresponding source of variation. The sign of the values indicate over- or underexpression in that factor depending on the sign of the corresponding gene weights in the amplitude matrix. As a result, the values can be plotted on the y axis against known covariates on the x axis to directly interpret the relationship between samples. When applied to GTEx, we observe one pattern associated with cerebellum, another pattern that has large positive values for one donor and large negative values for another donor, and eight other patterns associated with other sources of variation (supplemental information online).

I calculated the ICA with head()

        PC1       PC2
0  1.317276 -0.682285
1  1.696110 -0.549004
2  0.037709 -0.548736
3  0.702004 -0.545255
4  1.227363 -0.574219

but fail to see how the authors plotted their ICA graphs



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.