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edited Oct 18, 2019 at 9:45

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         Survival days  MTHFD1  SH3PXD2A    CAV1    ACTB    COL5A2  CDKN2C  BAG3    RALA    DST STEAP1  FZD1    IGFBP2  RBP1
GSM482796   1450    -0.538  0.261   0.368   0.671   0.194   -0.43   -0.179  0.551   -0.117  0.18    -0.527  -0.703  -0.0586
GSM482797   936 -0.209  0.097   -0.9    -0.307  0.0873  -0.516  -0.211  0.089   -0.0729 -0.0546 -0.132  -0.481  0.0215
GSM482798   936 -0.487  0.0853  -0.518  0.162   0.0326  -0.264  -0.0957 0.237   -0.0855 -0.243  -0.137  0.0581  0.11
GSM482799   2060    -0.355  0.0949  -0.198  0.232   0.0123  -0.506  0.0424  0.0626  0.128   0.0602  -0.538  -0.0969 0.277
GSM482800   2574    -0.547  0.0836  -0.81   -0.211  0.0928  -0.536  -0.301  0.126   -0.327  0.129   -0.251  0.536   0.02
GSM482801   2313    -0.484  -0.333  -1.13   0.312   -0.0508 -0.848  -0.0893 0.164   -0.15   -0.2    -0.85   0.0732  0.12
GSM482802   176 -0.343  0.194   1.29    0.436   0.221   -0.717  0.0727  0.65    1.29    0.857   0.00985 -0.384  0.289
GSM482803   NA  -0.623  0.176   -0.581  0.341   -0.0391 -0.446  -0.00736    -0.0541 -0.157  -0.197  -0.349  0.304   0.26
GSM482804   1327    -0.381  0.0195  -0.939  0.024   0.0151  -0.513  0.832   -0.055  0.0195  0.431   -0.673  -0.521  0.0575
GSM482805   1575    -0.167  0.0854  -0.411  0.0854  0.105   -0.296  0.101   0.31    0.798   -0.12   -0.152  0.119   0.142
GSM482806   687 -0.439  -0.0619 -1.06   0.0728  0.0771  -0.155  -0.232  0.164   -0.0181 0.196   0.449   0.748   -0.0259
GSM482807   736 -0.744  -0.191  -1.37   0.148   0.0684  -0.698  -0.292  0.187   -0.0628 -0.396  -0.598  -0.488  0.0977
GSM482808   816 -0.607  -0.194  -0.358  0.0134  0.159   -0.26   0.0238  -0.374  0.555   0.274   0.358   -0.0953 0.171
GSM482809   253 -0.354  0.121   -1.22   0.402   -0.0781 -0.699  -0.159  0.345   -0.0888 0.0523  -0.888  -0.759  0.0681
GSM482810   477 -0.607  -0.201  -1.05   0.551   -0.0554 -0.655  -0.148  -0.0741 -0.78   -0.31   -0.716  -0.154  0.0134
GSM482811   1035    -0.516  0.346   -0.62   0.0466  0.0884  -0.244  0.107   0.101   0.807   0.473   0.291   -0.417  0.0251
GSM482812   1984    -0.281  -0.0653 -0.917  0.255   -0.0167 -0.683  -0.0696 0.559   -0.175  -0.253  -0.458  -0.536  0.0461
GSM482813   2045    -0.42   0.0355  -0.792  0.513   0.158   -0.245  0.514   0.184   -0.211  -0.364  -0.573  0.183   0.049

> head(km)
    samples time        gene
1 GSM482796 1450 -0.11931980
2 GSM482797  936 -0.12209097
3 GSM482798  936 -0.10390257
4 GSM482799 2060 -0.07646939
5 GSM482800 2574 -0.16656837
6 GSM482801 2313 -0.12507939
>

> head(km)
     Sample Time        Gene Status
1 GSM482853   41  0.05649159    Low
2 GSM482857   41 -0.07667345    Low
3 GSM482866   54  0.10231150    Low
4 GSM482830   61 -0.05980938    Low
5 GSM482861   77  0.01231947    Low
6 GSM482818   78  0.21372177    Low
>

 fit <- survfit(Surv(Time, Status) ~ Gene, data = km)


> ggsurvplot(fit, data = km)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 70, 0, 140

         Survival days  MTHFD1  SH3PXD2A    CAV1    ACTB    COL5A2  CDKN2C  BAG3    RALA    DST STEAP1  FZD1    IGFBP2  RBP1
GSM482796   1450    -0.538  0.261   0.368   0.671   0.194   -0.43   -0.179  0.551   -0.117  0.18    -0.527  -0.703  -0.0586
GSM482797   936 -0.209  0.097   -0.9    -0.307  0.0873  -0.516  -0.211  0.089   -0.0729 -0.0546 -0.132  -0.481  0.0215
GSM482798   936 -0.487  0.0853  -0.518  0.162   0.0326  -0.264  -0.0957 0.237   -0.0855 -0.243  -0.137  0.0581  0.11
GSM482799   2060    -0.355  0.0949  -0.198  0.232   0.0123  -0.506  0.0424  0.0626  0.128   0.0602  -0.538  -0.0969 0.277
GSM482800   2574    -0.547  0.0836  -0.81   -0.211  0.0928  -0.536  -0.301  0.126   -0.327  0.129   -0.251  0.536   0.02
GSM482801   2313    -0.484  -0.333  -1.13   0.312   -0.0508 -0.848  -0.0893 0.164   -0.15   -0.2    -0.85   0.0732  0.12
GSM482802   176 -0.343  0.194   1.29    0.436   0.221   -0.717  0.0727  0.65    1.29    0.857   0.00985 -0.384  0.289
GSM482803   NA  -0.623  0.176   -0.581  0.341   -0.0391 -0.446  -0.00736    -0.0541 -0.157  -0.197  -0.349  0.304   0.26
GSM482804   1327    -0.381  0.0195  -0.939  0.024   0.0151  -0.513  0.832   -0.055  0.0195  0.431   -0.673  -0.521  0.0575
GSM482805   1575    -0.167  0.0854  -0.411  0.0854  0.105   -0.296  0.101   0.31    0.798   -0.12   -0.152  0.119   0.142
GSM482806   687 -0.439  -0.0619 -1.06   0.0728  0.0771  -0.155  -0.232  0.164   -0.0181 0.196   0.449   0.748   -0.0259
GSM482807   736 -0.744  -0.191  -1.37   0.148   0.0684  -0.698  -0.292  0.187   -0.0628 -0.396  -0.598  -0.488  0.0977
GSM482808   816 -0.607  -0.194  -0.358  0.0134  0.159   -0.26   0.0238  -0.374  0.555   0.274   0.358   -0.0953 0.171
GSM482809   253 -0.354  0.121   -1.22   0.402   -0.0781 -0.699  -0.159  0.345   -0.0888 0.0523  -0.888  -0.759  0.0681
GSM482810   477 -0.607  -0.201  -1.05   0.551   -0.0554 -0.655  -0.148  -0.0741 -0.78   -0.31   -0.716  -0.154  0.0134
GSM482811   1035    -0.516  0.346   -0.62   0.0466  0.0884  -0.244  0.107   0.101   0.807   0.473   0.291   -0.417  0.0251
GSM482812   1984    -0.281  -0.0653 -0.917  0.255   -0.0167 -0.683  -0.0696 0.559   -0.175  -0.253  -0.458  -0.536  0.0461
GSM482813   2045    -0.42   0.0355  -0.792  0.513   0.158   -0.245  0.514   0.184   -0.211  -0.364  -0.573  0.183   0.049

> head(km)
    samples time        gene
1 GSM482796 1450 -0.11931980
2 GSM482797  936 -0.12209097
3 GSM482798  936 -0.10390257
4 GSM482799 2060 -0.07646939
5 GSM482800 2574 -0.16656837
6 GSM482801 2313 -0.12507939
>

> head(km)
     Sample Time        Gene Status
1 GSM482853   41  0.05649159    Low
2 GSM482857   41 -0.07667345    Low
3 GSM482866   54  0.10231150    Low
4 GSM482830   61 -0.05980938    Low
5 GSM482861   77  0.01231947    Low
6 GSM482818   78  0.21372177    Low
>

 fit <- survfit(Surv(Time, Status) ~ Gene, data = km)


> ggsurvplot(fit, data = km)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 70, 0, 140

 fit <- survfit(Surv(Time, Status) ~ Gene, data = km)


> ggsurvplot(fit, data = km)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 70, 0, 140

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edited Oct 16, 2019 at 9:25

Zizogolu

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Doing kaplan meier plot with this data

I have normalized expression values of some genes in 76some patients and the how many days they have survived from their diagnosis with cancer like below

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edited Oct 11, 2019 at 13:44

Zizogolu

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EDITED

I divided patients based on the median of survival days to Up and Down category like below but still I am failing to visualize that

> head(km)
     Sample Time        Gene Status
1 GSM482853   41  0.05649159    Low
2 GSM482857   41 -0.07667345    Low
3 GSM482866   54  0.10231150    Low
4 GSM482830   61 -0.05980938    Low
5 GSM482861   77  0.01231947    Low
6 GSM482818   78  0.21372177    Low
>

 fit <- survfit(Surv(Time, Status) ~ Gene, data = km)


> ggsurvplot(fit, data = km)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 70, 0, 140

EDITED

I divided patients based on the median of survival days to Up and Down category like below but still I am failing to visualize that

> head(km)
     Sample Time        Gene Status
1 GSM482853   41  0.05649159    Low
2 GSM482857   41 -0.07667345    Low
3 GSM482866   54  0.10231150    Low
4 GSM482830   61 -0.05980938    Low
5 GSM482861   77  0.01231947    Low
6 GSM482818   78  0.21372177    Low
>

 fit <- survfit(Surv(Time, Status) ~ Gene, data = km)


> ggsurvplot(fit, data = km)
Error in data.frame(..., check.names = FALSE) : 
  arguments imply differing number of rows: 70, 0, 140

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edited Oct 11, 2019 at 11:33

Zizogolu

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edited Oct 11, 2019 at 10:40

Zizogolu

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edited Oct 11, 2019 at 10:33

Zizogolu

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asked Oct 10, 2019 at 15:58

Zizogolu

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Doing kaplan meier plot with this data

Doing kaplan meier plot with this data

Doing plot with this data