I'm trying to use the NanoStringDiff package to perform a differential gene expression analysis

However, when I try to construct the data set with the function NanoStringData = createNanoStringSetFromCsv(path, header = TRUE, designs), I keep receiving the error message "Error in rowSums(counts) : 'x' must be numeric"

Here it follows a section from my datasheet:

Name         Accession  Neg1  Neg2  Neg3  Neg4  Neg5  Neg6  Neg7  Neg8  Neg9 Neg10
1       Positive                POS_A(128)      ERCC_00117.1 45453 40894 34717 41316 70468 55628 59547 62007 46769 53269
2       Positive                 POS_B(32)      ERCC_00112.1 14424 12902 11005 13898 22849 18664 20197 20309 15565 17069
3       Positive                  POS_C(8)      ERCC_00002.1  3967  3666  3156  3887  6246  4990  5305  5460  4207  4723
4       Positive                  POS_D(2)      ERCC_00092.1   935   880   714   866  1501  1212  1222  1269   970  1140
5       Positive                POS_E(0.5)      ERCC_00035.1   157   120   141   150   246   193   193   185   135   178
6       Positive              POS_F(0.125)      ERCC_00034.1    67    59    43    53   117    86    95    84    78    83

Now, an example of my code and the error message:

directory <- "C:/Users/san_c/OneDrive/Área de Trabalho/Nanostring/Analise1_GCBHIV_GCBNEG"
path <- paste(directory, "datasetGCB.csv",sep="/")

NanoStringData = createNanoStringSetFromCsv(path, header = TRUE, designs)
Error in rowSums(counts) : 'x' must be numeric

R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

locale:
[1] LC_COLLATE=Portuguese_Brazil.1252  LC_CTYPE=Portuguese_Brazil.1252    LC_MONETARY=Portuguese_Brazil.1252
[4] LC_NUMERIC=C                       LC_TIME=Portuguese_Brazil.1252    

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

other attached packages:
[1] NanoStringDiff_1.4.0 Biobase_2.34.0       BiocGenerics_0.20.0 

loaded via a namespace (and not attached):
[1] tools_3.3.2        matrixStats_0.53.1

Does anyone else received this error message?

In section 3.1 from the NanoStringDiff vignette, they write

[...] you should create a csv.file to combine all interesting samples together, and the first three columns should be ”CodeClass”, ”Name” and ”Accession”, the counts data contained from the 4th column to the last column.

You could try to adapt your csv file to match the description above.