Hi, 

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... 
Computing pfp... 
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.

Thanks!!

Sumedha 

Duke University

SessionInfo():

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

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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RankProd_2.40.0

loaded via a namespace (and not attached):
[1] tools_3.2.0