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I'm new to analyzing scRNA-Seq data and ran into some problems while running the tutorial. Everything looks fine until I get to JackStrawPlot(pbmc, dims = 1:15). The p-values of each PC are the same as in the figure shown in the tutorial, except for PC 7, 12, and 15. Here is the JackStraw plot I generated:
compared to the plot from the tutorial:
Then, when I ran non-linear dimensional reduction (UMAP/tSNE) and plotted the results, I generated the following figure:
Several of the clusters (e.g. clusters 6 and 8) are shifted from their locations in the figure from the tutorial:
I copied and pasted the code from the tutorial into RStudio, so there should not be any differences in the code. I am not familiar with Python and Conda, so I suspect whatever I'm doing wrong has something to do with that. Any help explaining why I'm seeing differences in these plots would be greatly appreciated!
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I'm new to analyzing scRNA-Seq data and ran into some problems while running the tutorial. Everything looks fine until I get to
JackStrawPlot(pbmc, dims = 1:15)
. The p-values of each PC are the same as in the figure shown in the tutorial, except for PC 7, 12, and 15. Here is the JackStraw plot I generated:compared to the plot from the tutorial:
Then, when I ran non-linear dimensional reduction (UMAP/tSNE) and plotted the results, I generated the following figure:
Several of the clusters (e.g. clusters 6 and 8) are shifted from their locations in the figure from the tutorial:
I copied and pasted the code from the tutorial into RStudio, so there should not be any differences in the code. I am not familiar with Python and Conda, so I suspect whatever I'm doing wrong has something to do with that. Any help explaining why I'm seeing differences in these plots would be greatly appreciated!
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