Error in sqliteExecStatement(con, statement, bind.data) :
Hi All,
I seem to be having similar problems as everyone else and I have looked through many of the posts without finding the solution. However, I am new to R and RNA-seq in general.
Here is what I am getting in RStudio:
> cuff
CuffSet instance with:
4 samples
19856 genes
24928 isoforms
21518 TSS
23593 CDS
119136 promoters
129108 splicing
119136 relCDS
> disp<-dispersionPlot(gene(cuff))
Error in dispersionPlot(gene(cuff)) :
error in evaluating the argument 'object' in selecting a method for function 'dispersionPlot': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘gene’ for signature ‘"CuffSet"’
> disp<-dispersionPlot(genes(cuff))
> disp
Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 row, data has 0
In addition: Warning message:
In max(panels$ROW) : no non-missing arguments to max; returning -Inf
> genes.scv<-fpkmSCVPlot(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
> dens<-csDensity(genes(cuff))
> dens
Warning messages:
1: Removed 1414 rows containing non-finite values (stat_density).
2: Removed 2084 rows containing non-finite values (stat_density).
3: Removed 1457 rows containing non-finite values (stat_density).
4: Removed 1150 rows containing non-finite values (stat_density).
In particular, this error: Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
seems to be common with everyone. Has anyone figured out the cause and how to fix it?
I did add the gtfFile and genome arguments as suggested.
I would really appreciate any help. I am using v. 0.97551 of RStudio and Cuffdiff v. 2.1.1 on Galaxy.
Thanks,
Fres
Hi All,
I seem to be having similar problems as everyone else and I have looked through many of the posts without finding the solution. However, I am new to R and RNA-seq in general.
Here is what I am getting in RStudio:
> cuff
CuffSet instance with:
4 samples
19856 genes
24928 isoforms
21518 TSS
23593 CDS
119136 promoters
129108 splicing
119136 relCDS
> disp<-dispersionPlot(gene(cuff))
Error in dispersionPlot(gene(cuff)) :
error in evaluating the argument 'object' in selecting a method for function 'dispersionPlot': Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘gene’ for signature ‘"CuffSet"’
> disp<-dispersionPlot(genes(cuff))
> disp
Error in `$<-.data.frame`(`*tmp*`, "SCALE_X", value = 1L) :
replacement has 1 row, data has 0
In addition: Warning message:
In max(panels$ROW) : no non-missing arguments to max; returning -Inf
> genes.scv<-fpkmSCVPlot(genes(cuff))
Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
> dens<-csDensity(genes(cuff))
> dens
Warning messages:
1: Removed 1414 rows containing non-finite values (stat_density).
2: Removed 2084 rows containing non-finite values (stat_density).
3: Removed 1457 rows containing non-finite values (stat_density).
4: Removed 1150 rows containing non-finite values (stat_density).
In particular, this error: Error in sqliteExecStatement(con, statement, bind.data) :
RS-DBI driver: (error in statement: near ")": syntax error)
seems to be common with everyone. Has anyone figured out the cause and how to fix it?
I did add the gtfFile and genome arguments as suggested.
I would really appreciate any help. I am using v. 0.97551 of RStudio and Cuffdiff v. 2.1.1 on Galaxy.
Thanks,
Fres
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