I have used Tophat-CuffDiff pipeline so far but I want to give a try for DESeq2. I have 2 conditions and 3 replicates for each, aim is to find the differentially expressed genes.
For a couple of days, I am trying to use HTSeq to prepare my count files. I guess I did it but now I am stuck at creating the count table as the DESeq2 input.
I didn't use R that much so far, so I am having difficulties. Here is the problem:
Here is the 36 warnings:
Because it says "Gene IDs (first column) differ between files.", I have checked each file but all have the same number of rows and I guess the first column is same for all (well, I have used the same gtf file for all of them, so it must be).
I know the problem is at a very basic stage but I have no clue as an R-noob.
For a couple of days, I am trying to use HTSeq to prepare my count files. I guess I did it but now I am stuck at creating the count table as the DESeq2 input.
I didn't use R that much so far, so I am having difficulties. Here is the problem:
Code:
> library('DESeq2') Loading required package: GenomicRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: IRanges Loading required package: XVector Loading required package: Rcpp Loading required package: RcppArmadillo > setwd("C:/Python27/SKMEL-5") > directory<-"C:/Python27/SKMEL-5/ALL" > sampleFiles <- grep("SKMEL-5",list.files(directory),value=TRUE) > sampleCondition<-c("KD","KD","KD","WT","WT","WT") > sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition) > sampleTable sampleName fileName condition 1 SKMEL-5_I-1.txt SKMEL-5_I-1.txt KD 2 SKMEL-5_I-2.txt SKMEL-5_I-2.txt KD 3 SKMEL-5_I-3.txt SKMEL-5_I-3.txt KD 4 SKMEL-5_L-1.txt SKMEL-5_L-1.txt WT 5 SKMEL-5_L-2.txt SKMEL-5_L-2.txt WT 6 SKMEL-5_L-3.txt SKMEL-5_L-3.txt WT > ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition) Error in DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, : Gene IDs (first column) differ between files. In addition: There were 36 warnings (use warnings() to see them)
Code:
Warning messages: 1: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 2: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 3: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 4: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 5: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 6: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input 7: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 8: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 9: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 10: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 11: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 12: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input 13: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 14: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 15: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 16: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 17: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 18: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input 19: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 20: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 21: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 22: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 23: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 24: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input 25: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 26: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 27: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 28: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 29: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 30: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input 31: In read.table(file.path(directory, fn)) : line 1 appears to contain embedded nulls 32: In read.table(file.path(directory, fn)) : line 2 appears to contain embedded nulls 33: In read.table(file.path(directory, fn)) : line 3 appears to contain embedded nulls 34: In read.table(file.path(directory, fn)) : line 4 appears to contain embedded nulls 35: In read.table(file.path(directory, fn)) : line 5 appears to contain embedded nulls 36: In scan(file = file, what = what, sep = sep, quote = quote, ... : embedded nul(s) found in input
I know the problem is at a very basic stage but I have no clue as an R-noob.
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