NanoStringDiff counts not numeric
Entering edit mode
Last seen 3.4 years ago


I'm trying to use NanoStringDiff to analyse some Nanostring miRNA data. I am using the latest Bioconducter release (3.9) and R version 3.6.

My data is in a csv file. I am going to perform differential expression analysis to identify potential biomarkers.

Here is a section of my datasheet:

CodeClass   Name           Accession                Epi_FAM1.1  Epi_FAM1.2  Epi_FAM2    Epi_FAM3
Positive          POS_A(128)    ERCC_00117.1    77244                 77495     66892               68724
Positive          POS_B(32) ERCC_00112.1    20843                 22528     18344               19993
Positive          POS_C(8)         ERCC_00002.1 5065                  5758              4755                 5021
Positive          POS_D(2)         ERCC_00092.1 1452                  1450              1234                 1230

When I try to creat the set I get the error Error in rowSums(counts) : 'x' must be numeric, so I cannot proceed with analysis. If I import the datasheet to R and use is.numeric() each of the count columns returns TRUE.

Has anyone else had this issue?

##code and the error message:
> library("Biobase")
> library("NanoStringDiff")
> directory <- "c:/Users/noelleenright/Documents"
> path<-paste(directory,"TestNanoStringDiff.csv",sep="/")
> designs=data.frame(group=c('Epi', 'Epi',  'Epi',  'Epi'))
> NanoStringData=createNanoStringSetFromCsv(path,header = TRUE,designs)
Error in rowSums(counts) : 'x' must be numeric

> traceback()
3: rowSums(counts)
1: createNanoStringSetFromCsv(path, header = TRUE, designs)

> sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

Random number generation:
 RNG:     Mersenne-Twister 
 Normal:  Inversion 
 Sample:  Rounding 

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] NanoStringDiff_1.14.0 Biobase_2.44.0        BiocGenerics_0.30.0  

loaded via a namespace (and not attached):
[1] BiocManager_1.30.4 compiler_3.6.0     tools_3.6.0        yaml_2.2.0         Rcpp_1.0.1        
[6] matrixStats_0.54.0
NanoStringDiff • 776 views
Entering edit mode
Last seen 1 day ago
United States

The expectation is that your first three column headers will be 'Code.Class', 'Name', and 'Accession'.

Try fixing that and see if it helps.

Entering edit mode

Thats seems to have sorted the problem. Thanks very much. I had changed it from that to just CodeClass as that is in the pdf of instructions.


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