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Figured it out. Thank you! |
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I started the Seurat Guided Cluster Tutorial but I began to have issues replicated the graphs and figures made after the "Preform Linear Dimensional Reduction" section. I copy and pasted line for line from the tutorial and had all the same figures and values leading up to that section; however, when I run:
"print(pbmc[["pca"]], dims = 1:5, nfeatures = 5)"
I get :
PC_ 1
Positive: FTL, FTH1, CST3, AIF1, S100A4
Negative: MALAT1, IL32, LTB, IL7R, CCL5
PC_ 2
Positive: S100A8, S100A9, LYZ, CD14, LGALS2
Negative: B2M, NKG7, GZMA, CTSW, PRF1
PC_ 3
Positive: CD74, HLA-DRA, HLA-DPB1, HLA-DQA1, HLA-DQB1
Negative: PPBP, GNG11, SPARC, PF4, AP001189.4
PC_ 4
Positive: CD74, HLA-DQA1, HLA-DQB1, HLA-DQA2, HLA-DRA
Negative: FCGR3A, NKG7, FTL, RP11-290F20.3, S100A4
PC_ 5
Positive: FCGR3A, RP11-290F20.3, MS4A7, MALAT1, CKB
Negative: NKG7, LYZ, S100A9, S100A8, GNLY
Instead of:
PC_ 1
Positive: CST3, TYROBP, LST1, AIF1, FTL
Negative: MALAT1, LTB, IL32, IL7R, CD2
PC_ 2
Positive: CD79A, MS4A1, TCL1A, HLA-DQA1, HLA-DQB1
Negative: NKG7, PRF1, CST7, GZMB, GZMA
PC_ 3
Positive: HLA-DQA1, CD79A, CD79B, HLA-DQB1, HLA-DPB1
Negative: PPBP, PF4, SDPR, SPARC, GNG11
PC_ 4
Positive: HLA-DQA1, CD79B, CD79A, MS4A1, HLA-DQB1
Negative: VIM, IL7R, S100A6, IL32, S100A8
PC_ 5
Positive: GZMB, NKG7, S100A8, FGFBP2, GNLY
Negative: LTB, IL7R, CKB, VIM, MS4A7
And after that point, the PCA graphs are incorrect and the clusters have a different count and different shapes. If you could help that would be great.
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