I'm using the below code for samr to find down and up regulated genes
source("http://bioconductor.org/biocLite.R") biocLite(samr) data=celline.data #expression data imported from excel file whose columns are samples and rows are genes. First row has quantitative outcome. x=data[-1,] #expression data only without quantitative outcome y=data[1,] #Quantitative outcome library(samr) sam.data<-list(x=x,y=y, geneid= 1:nrow(data), genenames= row.names(data)) # prepare the data list required in “samr” #function samr.obj<-samr(sam.data, resp.type="Quantitative", nperms=100, random.seed=12345)
The last line is producing this error
Error in storage.mode(x) <- "double" :
(list) object cannot be coerced to type 'double'
In addition: Warning message:
In knnimp(x, k, maxmiss = rowmax, maxp = maxp) :
2950 rows with more than 50 % entries missing;
mean imputation used for these rows
Error during wrapup: cannot open the connection
I'll appreciate if someone can point out for me what I'm not doing right.