Hi,

Very new to R so be gentle. I am trying to do a differential analysis on 3 vs 3 (3 biological replicates).

This is my script using Rstudio:

library('DESeq2')
directory<-'/Users/htseq/A16_AE11'
sampleFiles<-list.files(directory)
sampleCondition<-c('A161','A162','A163','AE111','AE112','AE113')
sampleTable<-data.frame(sampleName=sampleFiles, fileName=sampleFiles, condition=sampleCondition)
ddsHTSeq<-DESeqDataSetFromHTSeqCount(sampleTable=sampleTable, directory=directory, design=~condition)
colData(ddsHTSeq)$condition<-factor(colData(ddsHTSeq)$condition, levels=c('A16','AE11'))
dds<-DESeq(ddsHTSeq, betaPrior=FALSE)
res<-results(dds)
res<-res[order(res$log2FoldChange),]
write.table(res,file='sim_condition_treated_results_deseq2.csv',sep = "\t",col.names = NA,quote = FALSE)

error when running "dds<-DESeq(ddsHTSeq, betaPrior=FALSE)" :

Error in designAndArgChecker(object, betaPrior) : 
  full model matrix is less than full rank

all my txt files are as follows (i will paste the start and finish of an example file) :

VIT_19s0177g003205  57
VIT_19s0177g003301  0
VIT_19s0177g003401  46
VIT_19s0177g003402  37
VIT_19s0177g003501  0
VIT_19s0177g003502  33
VIT_19s0177g003601  11
VIT_19s0177g003602  2
VIT_19s0177g003603  3
VIT_19s0177g003604  11
VIT_19s0177g003605  68
VIT_19s0177g003701  0
__no_feature    2031587
__ambiguous 13254821
__too_low_aQual 5245001
__not_aligned   1746024
__alignment_not_unique  1870124

EDIT: my bad...at sampleCondition<-c('A16','A16','A16','AE11','AE11','AE11')

thanks

Read over the vignette on this error. It has a specific section giving advice.