Question: NanoStringDiff counts not numeric
0
gravatar for noelleenright
6 months ago by
noelleenright0 wrote:

Hi

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)
2: whichis.na(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 

locale:
[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 • 114 views
ADD COMMENTlink modified 6 months ago by James W. MacDonald51k • written 6 months ago by noelleenright0
Answer: NanoStringDiff counts not numeric
0
gravatar for James W. MacDonald
6 months ago by
United States
James W. MacDonald51k wrote:

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

Try fixing that and see if it helps.

ADD COMMENTlink written 6 months ago by James W. MacDonald51k

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.

ADD REPLYlink written 6 months ago by noelleenright0
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