hi,

sorry what does this error mean pleas? i was going to binning the reads mapped on the genes by biophysconnector.

i have a ribo-seq bed file from tophat2 contains the gene IDS and start and end, a gene ids file from rna-seq and gene ids file from ribo-seq..i should first calculate the reads mapped on each gene then normalized the binned reads based on mapped reads from rna-seq...

but in the first step i got error

i shared my data...https://drive.google.com/drive/folders/0BwOX04QQkaXTM1lvS3N4THQyd3M

#input file containing the yeast gene IDs and length
genes <- as.data.frame(read.csv("geneID and length.txt",header = FALSE, sep=","),stringsAsFactors=FALSE)
genesID <- genes[,1]
geneslength <- genes[,2]
# building a matrix of footprint number
binwidth=100
#bed file containing the gene IDs and start and end of mapping
bed_table_FP <- as.data.frame(read.csv("footprint.bed",header = FALSE, sep="\t",stringsAsFactors=FALSE))
# creating a table containing the number of reads mapped on each genes
reads_table_FP <- as.data.frame(table(bed_table_FP[,1]))
# creating a table containing the number of reads mapped on each genes
GENES_COL <- as.vector(reads_table_FP[,1])
COUNTS_COL <- as.vector(reads_table_FP[,2])
MATRS <- cbind(GENES_COL, COUNTS_COL)
# ramp elimination, Consider only the rows that have the bed_table_FP column 3> 60
pos <-which(bed_table_FP[,3]>60)                                                                #####
bed_table_FP_new <- as.data.frame(bed_table_FP[pos,])    
# Create a new readstable based on the new bed_table
reads_table_FP_new <- as.data.frame(table(bed_table_FP_new[,1]))            
#Create Matrix with the count of reads mapping on each gene consider reads_table_FP_new
GENES_COL <- as.vector(reads_table_FP[,1])
COUNTS_COL <- as.vector(reads_table_FP[,2])
MATRS <- cbind(GENES_COL, COUNTS_COL)
#Create matrix that contains an ORF for each row and for each column that contains the count of reads that are in a window of n nucleotides
n=binwidth
MATRS_new_1 <- matrix(nrow=length(GENES_COL), ncol=(as.integer(max(geneslength)/n)+1))

Error in Summary.factor(c(1368L, 115L, 53L, 1135L, 1317L, 776L, 593L,  : 
  ‘max’ not meaningful for factors
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