I am trying to use RankProd to compare microarray data generated by me to some publicly available data. Therefore I am using RPadvance for 2 origins and 2 classes.
The command I ran:
RP.adv.out <- RPadvance(test, test.cl, test.origin, num.perm= 100, gene.names= test.gnames, rand=123)
where: "test" was read from a tab delimited .txt file containing both the datasets combined (common genes only) using the following commands
> test <- read.table("test_combined.txt", header= TRUE, sep="\t", stringsAsFactors=FALSE)
> rownames(test) <- test[,1]
> test <- test[,-1]
The typeof(test) is "double" and class(test) is "matrix". These data attributes are the SAME as the example data matrix provided with RankProd called arab. But somehow I feel that the error message (shown below) is due to mismatch of the expected vs actual data type.
Just fyi, the other input variables - test.cl, test.origin have the same number of entries as the number of columns, and are numeric vectors.
As I ran the RP.adv.out command, the output/error was as follows:
" The data is from 2 different origins
Rank Product analysis for two-class case
Starting 100 permutations...
Error in `row.names<-.data.frame`(`*tmp*`, value = value) :
invalid 'row.names' length"
I have been stuck with this for a really long time, so any help will be greatly appreciated.
R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):