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Issues: testing the findClusterMarkers function with dataset3 (adt198) #39

Open HsiaoChiLiao opened 1 year ago

HsiaoChiLiao commented 1 year ago

Hi Ray (@raymondlouie),

I am attaching an example subsample file (the final_out object) from dataset3 (adt198) that would run into an error with geneBasis when running findClusterMarkers. I reinstalled the package using devtools::install_github("https://github.com/raymondlouie/ClusterMarkers/tree/Dev") before running the command and that did not fix the issue.

3 things that I'd like to bring up here: 1) I selected method="citeFUSE", but the function seemed to run all 4 methods anyway. 2) No "xgboost" in the R Documentation when I typed?findClusterMarkers 3) Running geneBasis encountered an error (highlighted below)

Thanks!

> test <- findClusterMarkers(final_out$training_matrix,
+                            final_out$training_clusters,
+                            num_markers=15,
+                            method="citeFUSE",
+                            verbose=TRUE)
[broad_Failseed101_final_out_data3_adt198_all_equal_50subSamp10000_train.p0.5.Rds.zip](https://github.com/raymondlouie/ClusterMarkers/files/12258148/broad_Failseed101_final_out_data3_adt198_all_equal_50subSamp10000_train.p0.5.Rds.zip)

Methods used in this analysis: citeFuse, sc2marker, geneBasis, xgBoost

Caclulating markers using citeFuse.

Caclulating markers using sc2marker.

Warning: Non-unique features (rownames) present in the input matrix, making unique
Calculating Markers for T cells

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for B cells

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Unconventional T cells

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Dendritic cells

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for NK cells

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Monocytes

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Neutrophils

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Macrophages

 Using all genes as input.
  |====================================================================================| 100%
Calculating Markers for Megakaryocyte & erythroid cells

 Using all genes as input.
  |====================================================================================| 100%
15
1
CD90.2, TCRbchain, CD5, CD4, CD8b(Ly-3), CD27, CD3e, CD43, CD3, CD8a, CD62L, CD127(IL-7Ra), CD2, CD226(DNAM-1), CD73, CD270(HVEM), CD357(GITR), CD28, CD155(PVR), CD124(IL-4Ra), CD95(Fas), CD11a, CD103, CD278(ICOS), CD31, CD86, CD26(DPP-4), CD61, CD45, TCRVb8.1-8.2, Notch1, CD199(CCR9), CD45.2, CD278(ICOS).1, integrinb7, TCRVb5.1-5.2, CD150(SLAM), CD85k(gp49Receptor), Ly108, CD193(CCR3), Ly49H, CD93(AA4.1-earlyBlineage), CD55(DAF), CD314(NKG2D), CD169(Siglec-1), XCR1, CD48, CD370(CLEC9A-DNGR1), FolateReceptorb(FR-b), Ly49D, CD94, CD317(BST2-PDCA-1), CX3CR1, CD9, CD1d(CD1.1-Ly-38), NK-1.1, CD49a, CD274(B7-H1-PD-L1), CD20, CD41, CD106, CD115(CSF-1R), CD11b, CD11c, CD14, CD172a(SIRPa), CD200(OX2), CD272(BTLA), CD29, CD371(CLEC12A), CD39, CD49b, CD49d, CD80, F4-80, Ly-49A, Ly-6G-Ly-6C(Gr-1), Tim-4
2
CD19, CD45R-B220, IgD, CD23, CD21-CD35(CR2-CR1), CD22, CD24, CD38, CD55(DAF), CD79b(Igb), I-A-I-E, CD272(BTLA), CD185(CXCR5), Ly108, CD40, CD102, CD150(SLAM), CD1d(CD1.1-Ly-38), CD200(OX2), CD71, CD20, CD2, IgM, Ly-6A-E(Sca-1), CD31, CD138(Syndecan-1), CD93(AA4.1-earlyBlineage), CD44, CD26(DPP-4), CD278(ICOS).1, CD122(IL-2Rb), CD184(CXCR4), ESAM, CX3CR1, CD301a(MGL1), CD274(B7-H1-PD-L1), Ly49H, CD45, Ly-6G, CD159a(NKG2AB6), CD45.2, CD39, Ly49D, CD183(CXCR3), CD106, CD49a, CD29, CD103, CD115(CSF-1R), CD117(c-Kit), CD11b, CD11c, CD120b(TNFRTypeII-p75), CD127(IL-7Ra), CD14, CD155(PVR), CD172a(SIRPa), CD199(CCR9), CD28, CD3, CD304(Neuropilin-1), CD317(BST2-PDCA-1), CD357(GITR), CD36, CD3e, CD41, CD49b, CD51, CD61, CD80, CD86, CD9, CD94, CD95(Fas), F4-80, Ly-6C, Ly-6G-Ly-6C(Gr-1), NK-1.1, Tim-4
3
CD226(DNAM-1), CD73, CD183(CXCR3), CD49b, CD357(GITR), CD127(IL-7Ra), Ly-49A, CD43, CD11a, CD27, CD5, NK-1.1, CD61, CD44, CD278(ICOS), TCRr-d, CD94, CD29, CD122(IL-2Rb), CD48, CD186(CXCR6), CD54, CD2, Ly-6C, CD160, integrinb7, CD314(NKG2D), CD102, CD159a(NKG2AB6), TCRVr1.1-Cr4, CD28, CD278(ICOS).1, CD3, CD45, CD103, CD124(IL-4Ra), CD120b(TNFRTypeII-p75), CD51, CD274(B7-H1-PD-L1), CD279(PD-1), CD69, TCRVr2, CD169(Siglec-1), CD38, GITRLigand, IgM, CD137, TIGIT(Vstm3), CD140a, KCC2, CD193(CCR3), MERTK(Mer), CD45.1, CD201(EPCR), CD152, CD196(CCR6), CD317(BST2-PDCA-1), CD223(LAG-3), CD107a(LAMP-1), CD198(CCR8), ESAM, CD366(Tim-3), CD62P(P-selectin), anti-P2RY12, XCR1, CD182(CXCR2), CD200(OX2), CD301a(MGL1), Ly49H, Ly-6G-Ly-6C(Gr-1), CD14, CD150(SLAM), CD39, CD185(CXCR5), CD71, CD20, CD1d(CD1.1-Ly-38), CD41, CD11b, CD11c, CD172a(SIRPa), CD207(Langerin), CD371(CLEC12A), CD40, F4-80, PIR-A-B
4
CD11c, CD54, PIR-A-B, CD9, CD172a(SIRPa), I-A-I-E, CD371(CLEC12A), CD29, CD39, CD11b, CD44, CD49d, CD80, F4-80, CD317(BST2-PDCA-1), CD366(Tim-3), CD117(c-Kit), CD304(Neuropilin-1), CD4, CD48, CD326(Ep-CAM), CD26(DPP-4), XCR1, CD8a, CD106, ESAM, CD274(B7-H1-PD-L1), CD370(CLEC9A-DNGR1), CD301a(MGL1), CD155(PVR), CD86, CD40, CD107a(LAMP-1), CD120b(TNFRTypeII-p75), CD14, CD273(B7-DC-PD-L2), CD83, Tim-4, CD49a, SiglecH, CD62P(P-selectin), CD45.2, CD135, H-2KbboundtoSIINFEKL, CD270(HVEM), CD41, CD199(CCR9), CD200(OX2), CD200R(OX2R), CD68, CD115(CSF-1R), CD63, CD71, PanendothelialCellAntigen, CD207(Langerin), CD300LG(Nepmucin), CD150(SLAM), CD163, GABRB3, CD45, CD365(Tim-1), anti-P2RY12, IgM, CD16-32, CD192(CCR2), Ly108, CD152, Notch1, CD160, CD272(BTLA), CD69, ENPP1, IRF4, CD278(ICOS).1, GITRLigand, CD182(CXCR2), CD279(PD-1), CD200R3, CD15(SSEA-1), TCRVb5.1-5.2, TCRr-d, CD73, Ly-6G-Ly-6C(Gr-1), CD278(ICOS), CD103, CD20, CD122(IL-2Rb), CD127(IL-7Ra), CD183(CXCR3), CD22, CD3, CD357(GITR), CD3e, CD43, CD45R-B220, CD94, Ly-49A, Ly49D, NK-1.1
5
CD49b, NK-1.1, Ly49D, CD94, CD29, Ly49H, CD122(IL-2Rb), CD159a(NKG2AB6), CD11a, CD11b, CD43, KLRG1(MAFA), CD357(GITR), Ly-49A, CD54, CD314(NKG2D), CD335(NKp46), CD44, CD62L, CD2, CD64(FcrRI), CD106, CD49d, CD27, CD102, CD183(CXCR3), GITRLigand, PanendothelialCellAntigen, CD184(CXCR4), CD49a, CD45, F4-80, CD38, CD45.2, CD39, CD204(Msr1), CD62P(P-selectin), 4-1BBLigand(CD137L), IRF4, CD95(Fas), CD93(AA4.1-earlyBlineage), CD279(PD-1), anti-P2RY12, TER-119-ErythroidCells, CD270(HVEM), CD69, CD300LG(Nepmucin), CD48, CD309(VEGFR2-Flk-1), CD86, CD366(Tim-3), CD73, CD45R-B220, Ly-6G-Ly-6C(Gr-1), CD103, CD278(ICOS), CD127(IL-7Ra), CD124(IL-4Ra), CD155(PVR), CD20, CD25, CD3, CD371(CLEC12A), CD40, CD61, PIR-A-B
6
CD11b, CD115(CSF-1R), CX3CR1, Ly-6C, PIR-A-B, CD29, CD371(CLEC12A), CD172a(SIRPa), CD44, CD49d, CD49a, F4-80, CD36, CD9, CD41, CD14, CD11a, CD43, CD85k(gp49Receptor), CD304(Neuropilin-1), CD300LG(Nepmucin), CD61, CD107a(LAMP-1), CD106, CD120b(TNFRTypeII-p75), CD51, CD39, CD80, CD48, CD270(HVEM), CD163, CD64(FcrRI), CD93(AA4.1-earlyBlineage), P2X7R, CD54, CD45.2, CD198(CCR8), Tim-4, CD301b(MGL2), CD365(Tim-1), MERTK(Mer), CD105, CD223(LAG-3), CD45.1, CD193(CCR3), ESAM, CD134(OX-40), CD274(B7-H1-PD-L1), CD155(PVR), CD206(MMR), PanendothelialCellAntigen, CD102, CD62P(P-selectin), CD301a(MGL1), CD24, CD34.1, CD38, CD170(Singlec-F), CD1d(CD1.1-Ly-38), TIGIT(Vstm3), IL-33Ra(IL1RL1-ST2), CD197(CCR7), GITRLigand, GABRB3, CD278(ICOS).1, CD45, D62E(E-selectin), CD15(SSEA-1), IL-21Receptor, CD69, TCRVb8.1-8.2, CD152, XCR1, CD159a(NKG2AB6), TCRVb5.1-5.2, CD200(OX2), CD273(B7-DC-PD-L2), IgM, Ly49D, CD94, CD185(CXCR5), CD182(CXCR2), CD117(c-Kit), CD272(BTLA), CD3, CD40, CD138(Syndecan-1), CD127(IL-7Ra), I-A-I-E, CD278(ICOS), CD71, CD103, CD124(IL-4Ra), CD183(CXCR3), CD28, CD326(Ep-CAM), CD3e, NK-1.1
7
Ly-6G-Ly-6C(Gr-1), Ly-6G, PIR-A-B, CD44, CD61, CD9, CD182(CXCR2), CD172a(SIRPa), CD43, CD11a, CD371(CLEC12A), CD51, CD270(HVEM), CD24, CD41, Ly-6C, CD85k(gp49Receptor), CD62L, CD170(Singlec-F), CD29, CD115(CSF-1R), CD39, CD90.1(Thy-1.1), CD198(CCR8), CD200R3, CD192(CCR2), FceRIa, CD36, CD95(Fas), CD184(CXCR4), CD339(Jagged1), JAML, PanendothelialCellAntigen, CD105, CD107a(LAMP-1), CD279(PD-1), ESAM, CD206(MMR), CD106, CD117(c-Kit), CD63, CD163, CD300LG(Nepmucin), CD55(DAF), CD102, CD49d, CD103, CX3CR1, CD68, CD20, TCRVb5.1-5.2, CD28, CD71, CD199(CCR9), CD207(Langerin), CD38, CD25, CD278(ICOS), CD86, CD124(IL-4Ra), CD22, CD185(CXCR5), CD155(PVR), CD120b(TNFRTypeII-p75), CD127(IL-7Ra), CD159a(NKG2AB6), CD3, CD3e, CD40, CD54, CD94, Ly-49A, NK-1.1
8
Tim-4, CD106, F4-80, CD39, CD54, CD38, CD86, CD172a(SIRPa), CD14, PIR-A-B, FolateReceptorb(FR-b), CD107a(LAMP-1), MERTK(Mer), CD317(BST2-PDCA-1), CD80, CD64(FcrRI), CD4, CD9, CD193(CCR3), CD29, CD200(OX2), CD169(Siglec-1), P2X7R, CD63, CD105, PanendothelialCellAntigen, CD274(B7-H1-PD-L1), CD163, H-2KbboundtoSIINFEKL, CD44, CD301a(MGL1), CD201(EPCR), CD85k(gp49Receptor), TLR4(CD284)-MD2Complex, I-A-I-E, CD270(HVEM), CD200R(OX2R), CD20, CD192(CCR2), CD371(CLEC12A), CD304(Neuropilin-1), CX3CR1, CD68, CD49a, GABRB3, CD204(Msr1), CD196(CCR6), IRF4, CD16-32, CD115(CSF-1R), anti-P2RY12, CD31, ESAM, SiglecH, GITRLigand, CD223(LAG-3), XCR1, CD41, CD278(ICOS), IL-33Ra(IL1RL1-ST2), CD134(OX-40), CD48, CD62P(P-selectin), CD24, Notch1, CD278(ICOS).1, CD279(PD-1), CD28, Ly-6A-E(Sca-1), FceRIa, CD79b(Igb), CD184(CXCR4), CD194(CCR4), CD185(CXCR5), CD370(CLEC9A-DNGR1), CD159a(NKG2AB6), TCRr-d, CD137, TCRVr1.1-Cr4, CD8a, Ly49H, TCRVb5.1-5.2, CD199(CCR9), CD124(IL-4Ra), CD186(CXCR6), CD103, CD3, CD45.2, CD127(IL-7Ra), CD183(CXCR3), CD25, CD3e, CD73, CD94, Ly-49A, Ly-6C, NK-1.1
9
TER-119-ErythroidCells, CD71, CD24, CD270(HVEM), IgD, CD45R-B220, CD90.1(Thy-1.1), CD38, CD197(CCR7), CD55(DAF), CD21-CD35(CR2-CR1), Slc7a1(Cat-1-ERR), CD64(FcrRI), IL-33Ra(IL1RL1-ST2), CD79b(Igb), CD196(CCR6), CD194(CCR4), CD204(Msr1), CD23, TLR4(CD284)-MD2Complex, Notch4, CD365(Tim-1), CD206(MMR), CD252(OX40Ligand), IL-21Receptor, 4-1BBLigand(CD137L), D62E(E-selectin), Ly-49A, CD193(CCR3), CD20, CD51, anti-P2RY12, CD253(TRAIL), CD34.1, CD69, CD198(CCR8), CD93(AA4.1-earlyBlineage), CD170(Singlec-F), TCRVr3, FolateReceptorb(FR-b), ENPP1, CX3CR1, FceRIa, CD314(NKG2D), CD40, CD138(Syndecan-1), CD195(CCR5), TCRVb8.1-8.2, F4-80, CD150(SLAM), H-2KbboundtoSIINFEKL, CD95(Fas), CD3e, CD16-32, CD160, CD317(BST2-PDCA-1), CD85k(gp49Receptor), CD29, Ly-6C, CD45.2, Ly-6A-E(Sca-1), IRF4, CD199(CCR9), CD371(CLEC12A), CD86, CD49d, CD43, CD3, CD103, CD73, CD44, CD274(B7-H1-PD-L1), CD115(CSF-1R), CD120b(TNFRTypeII-p75), CD155(PVR), CD207(Langerin), CD25, CD27, CD273(B7-DC-PD-L2), CD278(ICOS), CD357(GITR), Ly49D
10
TCRbchain, CD5, CD4, CD8b(Ly-3), CD27, CD3e, CD43, CD3, CD8a, CD62L, CD127(IL-7Ra), CD2, CD73, CD270(HVEM), CD357(GITR), CD28, CD155(PVR), CD124(IL-4Ra), CD95(Fas), CD11a, CD103, CD278(ICOS), CD31, CD86, CD26(DPP-4), CD61, CD45, TCRVb8.1-8.2, Notch1, CD199(CCR9), CD45.2, CD278(ICOS).1, integrinb7, TCRVb5.1-5.2, CD150(SLAM), CD85k(gp49Receptor), Ly108, CD193(CCR3), Ly49H, CD93(AA4.1-earlyBlineage), CD55(DAF), CD314(NKG2D), CD169(Siglec-1), XCR1, CD48, CD370(CLEC9A-DNGR1), FolateReceptorb(FR-b), Ly49D, CD94, CD317(BST2-PDCA-1), CX3CR1, CD9, CD1d(CD1.1-Ly-38), NK-1.1, CD49a, CD274(B7-H1-PD-L1), CD20, CD41, CD106, CD115(CSF-1R), CD14, CD172a(SIRPa), CD200(OX2), CD272(BTLA), CD29, CD371(CLEC12A), CD39, CD49d, CD80, F4-80, Ly-49A
11
CD45R-B220, IgD, CD23, CD21-CD35(CR2-CR1), CD22, CD24, CD38, CD55(DAF), CD79b(Igb), I-A-I-E, CD272(BTLA), CD185(CXCR5), Ly108, CD40, CD102, CD150(SLAM), CD1d(CD1.1-Ly-38), CD200(OX2), CD71, CD20, CD2, IgM, Ly-6A-E(Sca-1), CD31, CD138(Syndecan-1), CD93(AA4.1-earlyBlineage), CD44, CD26(DPP-4), CD278(ICOS).1, CD122(IL-2Rb), CD184(CXCR4), ESAM, CX3CR1, CD301a(MGL1), CD274(B7-H1-PD-L1), Ly49H, CD45, Ly-6G, CD159a(NKG2AB6), CD45.2, CD39, Ly49D, CD183(CXCR3), CD106, CD49a, CD29, CD103, CD115(CSF-1R), CD117(c-Kit), CD120b(TNFRTypeII-p75), CD127(IL-7Ra), CD14, CD155(PVR), CD172a(SIRPa), CD199(CCR9), CD28, CD3, CD304(Neuropilin-1), CD317(BST2-PDCA-1), CD357(GITR), CD36, CD3e, CD41, CD51, CD61, CD80, CD86, CD9, CD94, CD95(Fas), F4-80, Ly-6C, NK-1.1
12
CD73, CD183(CXCR3), CD357(GITR), CD127(IL-7Ra), Ly-49A, CD43, CD11a, CD27, CD5, NK-1.1, CD61, CD44, CD278(ICOS), TCRr-d, CD94, CD29, CD122(IL-2Rb), CD48, CD186(CXCR6), CD54, CD2, Ly-6C, CD160, integrinb7, CD314(NKG2D), CD102, CD159a(NKG2AB6), TCRVr1.1-Cr4, CD28, CD278(ICOS).1, CD3, CD45, CD103, CD124(IL-4Ra), CD120b(TNFRTypeII-p75), CD51, CD274(B7-H1-PD-L1), CD279(PD-1), CD69, TCRVr2, CD169(Siglec-1), CD38, GITRLigand, IgM, CD137, TIGIT(Vstm3), CD140a, KCC2, CD193(CCR3), MERTK(Mer), CD45.1, CD201(EPCR), CD152, CD196(CCR6), CD317(BST2-PDCA-1), CD223(LAG-3), CD107a(LAMP-1), CD198(CCR8), ESAM, CD366(Tim-3), CD62P(P-selectin), anti-P2RY12, XCR1, CD182(CXCR2), CD200(OX2), CD301a(MGL1), Ly49H, CD14, CD150(SLAM), CD39, CD185(CXCR5), CD71, CD20, CD1d(CD1.1-Ly-38), CD41, CD172a(SIRPa), CD207(Langerin), CD371(CLEC12A), CD40, F4-80, PIR-A-B
13
CD54, PIR-A-B, CD9, CD172a(SIRPa), I-A-I-E, CD371(CLEC12A), CD29, CD39, CD44, CD49d, CD80, F4-80, CD317(BST2-PDCA-1), CD366(Tim-3), CD117(c-Kit), CD304(Neuropilin-1), CD4, CD48, CD326(Ep-CAM), CD26(DPP-4), XCR1, CD8a, CD106, ESAM, CD274(B7-H1-PD-L1), CD370(CLEC9A-DNGR1), CD301a(MGL1), CD155(PVR), CD86, CD40, CD107a(LAMP-1), CD120b(TNFRTypeII-p75), CD14, CD273(B7-DC-PD-L2), CD83, CD49a, SiglecH, CD62P(P-selectin), CD45.2, CD135, H-2KbboundtoSIINFEKL, CD270(HVEM), CD41, CD199(CCR9), CD200(OX2), CD200R(OX2R), CD68, CD115(CSF-1R), CD63, CD71, PanendothelialCellAntigen, CD207(Langerin), CD300LG(Nepmucin), CD150(SLAM), CD163, GABRB3, CD45, CD365(Tim-1), anti-P2RY12, IgM, CD16-32, CD192(CCR2), Ly108, CD152, Notch1, CD160, CD272(BTLA), CD69, ENPP1, IRF4, CD278(ICOS).1, GITRLigand, CD182(CXCR2), CD279(PD-1), CD200R3, CD15(SSEA-1), TCRVb5.1-5.2, TCRr-d, CD278(ICOS), CD103, CD20, CD122(IL-2Rb), CD127(IL-7Ra), CD183(CXCR3), CD22, CD3, CD357(GITR), CD3e, CD43, CD94, Ly-49A, Ly49D, NK-1.1
14
NK-1.1, Ly49D, CD94, CD29, Ly49H, CD122(IL-2Rb), CD159a(NKG2AB6), CD11a, CD43, KLRG1(MAFA), CD357(GITR), Ly-49A, CD314(NKG2D), CD335(NKp46), CD44, CD62L, CD2, CD64(FcrRI), CD106, CD49d, CD27, CD102, CD183(CXCR3), GITRLigand, PanendothelialCellAntigen, CD184(CXCR4), CD49a, CD45, F4-80, CD38, CD45.2, CD39, CD204(Msr1), CD62P(P-selectin), 4-1BBLigand(CD137L), IRF4, CD95(Fas), CD93(AA4.1-earlyBlineage), CD279(PD-1), anti-P2RY12, CD270(HVEM), CD69, CD300LG(Nepmucin), CD48, CD309(VEGFR2-Flk-1), CD86, CD366(Tim-3), CD103, CD278(ICOS), CD127(IL-7Ra), CD124(IL-4Ra), CD155(PVR), CD20, CD25, CD3, CD371(CLEC12A), CD40, CD61, PIR-A-B
15
CD115(CSF-1R), CX3CR1, Ly-6C, PIR-A-B, CD29, CD371(CLEC12A), CD172a(SIRPa), CD44, CD49d, CD49a, F4-80, CD36, CD9, CD41, CD14, CD11a, CD43, CD85k(gp49Receptor), CD304(Neuropilin-1), CD300LG(Nepmucin), CD61, CD107a(LAMP-1), CD106, CD120b(TNFRTypeII-p75), CD51, CD39, CD80, CD48, CD270(HVEM), CD163, CD64(FcrRI), CD93(AA4.1-earlyBlineage), P2X7R, CD45.2, CD198(CCR8), CD301b(MGL2), CD365(Tim-1), MERTK(Mer), CD105, CD223(LAG-3), CD45.1, CD193(CCR3), ESAM, CD134(OX-40), CD274(B7-H1-PD-L1), CD155(PVR), CD206(MMR), PanendothelialCellAntigen, CD102, CD62P(P-selectin), CD301a(MGL1), CD24, CD34.1, CD38, CD170(Singlec-F), CD1d(CD1.1-Ly-38), TIGIT(Vstm3), IL-33Ra(IL1RL1-ST2), CD197(CCR7), GITRLigand, GABRB3, CD278(ICOS).1, CD45, D62E(E-selectin), CD15(SSEA-1), IL-21Receptor, CD69, TCRVb8.1-8.2, CD152, XCR1, CD159a(NKG2AB6), TCRVb5.1-5.2, CD200(OX2), CD273(B7-DC-PD-L2), IgM, Ly49D, CD94, CD185(CXCR5), CD182(CXCR2), CD117(c-Kit), CD272(BTLA), CD3, CD40, CD138(Syndecan-1), CD127(IL-7Ra), I-A-I-E, CD278(ICOS), CD71, CD103, CD124(IL-4Ra), CD183(CXCR3), CD28, CD326(Ep-CAM), CD3e

**Caclulating markers using geneBasis.

Error in fun(arg) : sce should have unique rownames.**
In addition: Warning messages:
1: In findClusterMarkers(final_out$training_matrix, final_out$training_clusters,  :
  No method or invalid method selected. Using all methods.

2: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
3: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
4: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
5: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
6: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
7: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
8: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
9: In mean.fxn(object[features, cells.1, drop = FALSE]) : NaNs produced
HsiaoChiLiao commented 1 year ago

broad_Failseed101_final_out_data3_adt198_all_equal_50subSamp10000_train.p0.5.Rds.zip

raymondlouie commented 1 year ago

Thanks Hsiao Chi and sorry for the late reply. I suspect the issue with geneBasis is because there are duplicate protein names. I encountered the same issue, and I fixed it by making the names unique. But you raised a good point, I'll fix the code and output a warning message, and I'll have a look at the other issues you raised later.