edgeR error: arguments imply differing number of rows: 4211, 4216

Question

[zh.khodadadi]

Hi I wanted to analyze my bacteria RNA seq data .it has two condition and 2 replication. for analysis i use sparta(Simple Program for Automated reference-based bacterial RNA-seq Transcriptome Analysis).trimommatics,bowtie2,htseq and edgeR are in this workflow. in edgeR i get an error: Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 4211, 4216 by command alldata <- cbind(Cont9295_1,Cont9294_2,Case15m9283_1,Case15m9284_2) this error s normal? how to resolve it? thank for your help.

[h.mon]

More detail from you - like commands used, if you used only one or more references, etc - would help.

It seems one or more samples have a different number of genes, check the length / dimensions of whatever object (vector, matrix?) holding your counts:

length(Cont9295_1)
length(Cont9294_2)
...

or

dim(Case15m9283_1)
dim(Case15m9284_2)
...

[zh.khodadadi]

the samples belong a control(just one reference condition) and a case with two replication. I do DE analysis whit Rockhoper2 and get DE genes. sparta is automated and I run it with default htseq command(--stranded= no --minqual=10 --type=exon --mode=union). edgeR command:

*> library('limma')

library('edgeR') Cont9295_1 <- read.table('/home/user/Desktop/RNAseq_Data/2017-03-08/DEanalysis/mapCont9295.sam', row.names=1) colnames(Cont9295_1) <- 'Cont9295_1' Cont9294_2 <- read.table('/home/user/Desktop/RNAseq_Data/2017-03-08/DEanalysis/mapCont9294.sam', row.names=1) colnames(Cont9294_2) <- 'Cont9294_2' Case15m9283_1 <- read.table('/home/user/Desktop/RNAseq_Data/2017-03-08/DEanalysis/mapCase15m9283.sam', row.names=1) colnames(Case15m9283_1) <- 'Case15m9283_1' Case15m9284_2 <- read.table('/home/user/Desktop/RNAseq_Data/2017-03-08/DEanalysis/mapCase15m9284.sam', row.names=1) colnames(Case15m9284_2) <- 'Case15m9284_2' alldata <- cbind(Cont9295_1,Cont9294_2,Case15m9283_1,Case15m9284_2) Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 4211, 4216* Sparta command: SPARTA.py --cleanup --threads=8 --clip=TruSeq3-SE.fa:2:40:15 --stranded=no --type=exon

[h.mon]

Are you sure you should use read.table() to read a SAM alignment?

[zh.khodadadi]

sorry for delay yes because i wanted to run sparta and sparta scripts use this function. i apply these commands exactly like sparta. for sparta example works right. can you help me for new edgeR code ? other functions or code for rna seq data.

[zh.khodadadi]

this is sparta site: http://sparta-teaching.readthedocs.io/en/latest/

[Michael]

Possibly this is very important information, which should have been given immediately. In fact, by without providing all relevant information you must be aware that you are wasting the time of everyone who is trying to help you.

The crucial point is that you are using the package in a non-standard way, through another pipeline.

[zh.khodadadi]

i see the edgeR site for make sure. read table () uses to read a SAM. from edger: we need to read the files into RStudio. To do this we need to create a variable for each file. I will give an example for each treatment that you should be able to copy and paste into RStudio. Mac users: For LB control: wt1 = read.table(“~/Desktop/mapLRLB1.sam”, row.names=1)