Unknown or uninitialised column: 'geneset.names'.

[elcega]

I have created the three gene expression matrix (gem), design data matrix (ddm) and gmt.

> head(gem)
             S1           S2           S3           S4           S5           S6
A1 0.0006931562 0.0006773538 0.0007278626 6.508220e-04 9.083433e-04 1.126689e-03
A2 0.0019153881 0.0019366267 0.0014765212 1.573681e-03 2.584282e-03 7.389090e-03
...


> head(gmt_gmt)
# A tibble: 3 x 94
  GeneSet Description ...3  ...4  ...5  ...6  ...7  ...8  ...9  ...10 ...11 ...12 ...13
  <chr>   <chr>       <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
1 AA      Up_mid      A1    A2    A3    A4    A5    A6    A7    A8    A9    A10   A11  
2 BB      Up_west     B1    B2    B3    B4    B5    B6    B7    B8    B9    B10   B11  
3 CC      Up_east     C1    C2    C3    C4    C5    C6    C7    C8    C9    C10   C11 


> head(ddm)
# A tibble: 6 x 3
  Sample Location Station
  <chr>  <chr>      <dbl>
1 S1     West           1
2 S2     West           1
3 S3     West           2

identical(ncol(gem), nrow(ddm))
#> [1] TRUE

I have run the following:

TcGSA::plot1GS(expr = gem, 
               #plot1GS(expr = tcgsa_result$Estimations,
               gmt = gmt_gmt, 
               Subject_ID = ddm$Location, 
               TimePoint = ddm$Station,
               clustering = FALSE, 
               time_unit = "W", 
               geneset.name = gmt_gmt$GeneSet, 
               title="",
               margins=0.4,
               lab.cex=0.37,
               axis.cex=0.37,
               line.size=0.45,
               gg.add=list(ggplot2::theme(legend.position="none"),
                        ggplot2::ylim(-1.26,1.26)
               ))

And obtain the following error

Unknown or uninitialised column: 'geneset.names'.Error in TcGSA::plot1GS(expr = gem, gmt = gmt_gmt, Subject_ID = ddm$Location, :
The 'geneset.name' supplied is not in the 'gmt'

How is it possible? I haven't run any likelihood ratio tests and went straight to the graphical outputs (not sure if it matters).

[elcega]

I followed steps as shown in here:
https://cran.r-project.org/web/packages/TcGSA/vignettes/TcGSA_userguide.html

[borishejblum]

Hi Elena,

Thanks for you interest in our work.

Unfortunatley, TcGSA is not a visualization tool, it is a statistical method to perform Gene Set Analysis (hence the likelihood ratios) of longitudinal microarray gene expression data.
It has some plotting capapbilities built using ggplot2, but those are specifically designed to visualize and interpret the output of the statistical method.

The error you are getting specifically comes from the gmt object you are using which does not seem to have the right format (TcGSA expects a list of lists, not a tibble -- see GSA::GSA.read.gmt() for more information).

Since it seem you do not have microarray data and have solely interested in visualization, I would advize that you turn to visualization software such the ggplot2 package itself.

Best,
Boris