1. 第一次样本比较多，ssGSEA和String都没有运行出来，allprint显示：
[1] "The filePath..."
[1] "/home//ubuntu//mainhome//sxdata//user_file//f0b7047e391635ce5084b33fc0e562d7//20240213234140904/"
[1] "The saveDir..."
[1] "/home/ubuntu/mainhome/sxdata/user_file/f0b7047e391635ce5084b33fc0e562d7/20240213234140904result"
[1] "start to run checkError!"
[1] "Rownames to geneSymbol done!"
NULL
checkError processing over...
[1] "All R compute finishes successfully."
processResult.server over...
[1] "start to source function!"
[1] "/home/ubuntu/mainhome/sxdata/project/tool.data/immnue/TIP//3.ImmuneInfiltration/1.CIBERSORT.server.R"
[1] "/home/ubuntu/mainhome/sxdata/project/tool.data/immnue/TIP//2.ImmuneActivityScore/immunityScore.server.R"
[1] "start to run immunityScore.server!"
[1] "source is end"
[1] "set.seed"
[1] "read down!"
named integer(0)
Step1 Step2.negative
"(38/40)" "(3/3)"
Step2.positive Step3.negative
"(32/33)" "(18/18)"
Step3.positive Step4.T cell.recruiting
"(44/44)" "(10/10)"
Step4.CD4 T cell.recruiting Step4.CD8 T cell.recruiting
"(3/3)" "(8/8)"
Step4.Th1 cell.recruiting Step4.Dendritic cell.recruiting
"(4/4)" "(5/5)"
Step4.Th22 cell.recruiting Step4.Macrophage.recruiting
"(2/2)" "(5/5)"
Step4.Monocyte.recruiting Step4.Neutrophil.recruiting
"(3/3)" "(6/6)"
Step4.NK cell.recruiting Step4.Eosinophil.recruiting
"(8/8)" "(3/3)"
Step4.Basophil.recruiting Step4.Th17 cell.recruiting
"(2/2)" "(4/4)"
Step4.B cell.recruiting Step4.Th2 cell.recruiting
"(2/2)" "(3/3)"
Step4.Treg cell.recruiting Step4.MDSC.recruiting
"(6/6)" "(2/2)"
Step5.negative Step5.positive
"(5/5)" "(4/4)"
Step6.negative Step6.positive
"(6/6)" "(18/19)"
Step7.negative Step7.positive
"(22/22)" "(3/3)"
Processing wrong...
[1] "immunityScore.server is end"
[1] "start to run CIBERSORT.server!"
[1] "The Infiltration source codes is import!"
[1] "The user data is import!"
[1] "The signature matrix is import!"
[1] "CIBERSORT.server is end"
[1] "the TIP_integration is end !"
TIP process over...
[1] "The filePath..."
[1] "/home//ubuntu//mainhome//sxdata//user_file//f0b7047e391635ce5084b33fc0e562d7//20240213234140904/"
[1] "The saveDir..."
[1] "/home/ubuntu/mainhome/sxdata/user_file/f0b7047e391635ce5084b33fc0e562d7/20240213234140904result"
[1] "start to run checkError!"
[1] "Rownames to geneSymbol done!"
NULL
checkError processing over...
[1] "All R compute finishes successfully."
processResult.server over...
[1] "start to source function!"
[1] "/home/ubuntu/mainhome/sxdata/project/tool.data/immnue/TIP//3.ImmuneInfiltration/1.CIBERSORT.server.R"
[1] "/home/ubuntu/mainhome/sxdata/project/tool.data/immnue/TIP//2.ImmuneActivityScore/immunityScore.server.R"
[1] "start to run immunityScore.server!"
[1] "source is end"
[1] "set.seed"
[1] "read down!"
named integer(0)
Step1 Step2.negative
"(38/40)" "(3/3)"
Step2.positive Step3.negative
"(32/33)" "(18/18)"
Step3.positive Step4.T cell.recruiting
"(44/44)" "(10/10)"
Step4.CD4 T cell.recruiting Step4.CD8 T cell.recruiting
"(3/3)" "(8/8)"
Step4.Th1 cell.recruiting Step4.Dendritic cell.recruiting
"(4/4)" "(5/5)"
Step4.Th22 cell.recruiting Step4.Macrophage.recruiting
"(2/2)" "(5/5)"
Step4.Monocyte.recruiting Step4.Neutrophil.recruiting
"(3/3)" "(6/6)"
Step4.NK cell.recruiting Step4.Eosinophil.recruiting
"(8/8)" "(3/3)"
Step4.Basophil.recruiting Step4.Th17 cell.recruiting
"(2/2)" "(4/4)"
Step4.B cell.recruiting Step4.Th2 cell.recruiting
"(2/2)" "(3/3)"
Step4.Treg cell.recruiting Step4.MDSC.recruiting
"(6/6)" "(2/2)"
Step5.negative Step5.positive
"(5/5)" "(4/4)"
Step6.negative Step6.positive
"(6/6)" "(18/19)"
Step7.negative Step7.positive
"(22/22)" "(3/3)"
Processing wrong...
[1] "immunityScore.server is end"
[1] "start to run CIBERSORT.server!"
[1] "The Infiltration source codes is import!"
[1] "The user data is import!"
[1] "The signature matrix is import!"
[1] "CIBERSORT.server is end"
[1] "the TIP_integration is end !"
TIP process over...
2.第二次，删减样本，再次去重（之前也有去重）
Error in TIP_integration(codePath = "/project/tool.data/immnue/TIP/", :
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
cannot open compressed file '/expression.afterIDConvert.RData', probable reason 'No such file or directory'
Execution halted
