seurat probelm

Question

[Andy]

Good afternoon,

I got an error from R/4.0.0 after I run RunHarmony.

My code is:

combine_datalist<-RunHarmony(combine_datalist, "stim", assay.use="SCT")

The error is:

Error in Seurat::FetchData(object, group.by.vars) : 
  None of the requested variables were found: stim

I also tried to modified my code:

combine_datalist<-RunHarmony(combine_datalist, group.by.vars="sample_id", assay.use="SCT", max.iter.harmony=10)

The error is:

Error in Seurat::FetchData(object, group.by.vars) : 
  None of the requested variables were found: sample_id

Before I runHarmony, I run PCA. My out put is:

PC_ 1 
Positive:  MALAT1, DCN, HSPA1A, MT1H, GPX3, CFD, MT1G, FTL, ALDOB, TMSB4X 
       HLA-DRA, CCL4, B2M, CXCL14, CD74, GNLY, HSPA6, NKG7, FTH1, CCL5 
       HSP90AA1, COL1A2, CXCL2, MGP, IL8, MIOX, MT2A, S100A6, APOE, S100A9 
Negative:  PRSS1, CLPS, CTRB1, CPA1, PNLIP, CPB1, CELA3A, CELA3B, CTRC, PLA2G1B 
       CEL, CELA2A, AMY2A, REG1A, SPINK1, SYCN, GP2, CPA2, CTRB2, PRSS3 
       CELA2B, AMY2B, KLK1, CTRL, PNLIPRP1, REG1B, CUZD1, IGFBP2, PDIA2, ERP27 
PC_ 2 
Positive:  MT1G, MT1H, ALDOB, GPX3, MT1F, MIOX, MT1X, FTL, PCK1, GSTA1 
       MT1E, FABP1, CRYAB, HPD, PDZK1IP1, RBP5, GATM, FXYD2, SPP1, MT2A 
       SUCLG1, GSTA2, APOE, NAT8, BHMT, DCXR, CYB5A, BBOX1, PEBP1, S100A1 
Negative:  MALAT1, DCN, CFD, HSPA1A, MGP, HLA-DRA, CCL4, COL1A2, TMSB4X, COL1A1 
       LUM, IGFBP7, CD74, B2M, HSPA6, GNLY, IL8, CXCL2, COL3A1, S100A9 
       C11orf96, GSN, FBLN1, CCL5, JUN, HSPA1B, NKG7, HLA-DPB1, FOS, DNAJB1 

Please give me some suggestions to solve this problem. Thanks a lot.

[rpolicastro]

Does the sample_id metadata column exist in your data?

[Andy]

I understand where I got wrong. Thanks