I'm working on combining multiple mouse samples from two different sequencing runs (same tissue). I am combining the samples across sequencing runs as outlined in the tutorials into one snap object (4 samples from one run and 2 samples from another run for a total of 6 samples). For some reason after dimensional reduction there is no shape/structure to the eigenvector pairwise plots (as shown below). However, when I keep the two runs as separate snap objects, the plots show up as we would normally expect and I am able to choose the correct number of significant eigenvectors for analysis. I'm wondering if there's any reason for this? The same mm10 reference was used in both cases, so the data should be fairly similar between the two.
Thank you in advance for any help you may be able to provide!
Molly
I'm working on combining multiple mouse samples from two different sequencing runs (same tissue). I am combining the samples across sequencing runs as outlined in the tutorials into one snap object (4 samples from one run and 2 samples from another run for a total of 6 samples). For some reason after dimensional reduction there is no shape/structure to the eigenvector pairwise plots (as shown below). However, when I keep the two runs as separate snap objects, the plots show up as we would normally expect and I am able to choose the correct number of significant eigenvectors for analysis. I'm wondering if there's any reason for this? The same mm10 reference was used in both cases, so the data should be fairly similar between the two.
Thank you in advance for any help you may be able to provide! Molly