DEGseq for multiple samples

Question

[ALOUSH ALI]

I am using DEGseq package with DEGexp with MARS option. So i am trying to recall the example that the manual provide

library(DEGseq)
geneExpFile <- system.file("extdata", "GeneExpExample5000.txt", package="DEGseq")
geneExpMatrix1 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(7,9,12,15,18))
geneExpMatrix2 <- readGeneExp(file=geneExpFile, geneCol=1, valCol=c(8,10,11,13,16))
head(geneExpMatrix1)

Results

##                 EnsemblGeneID     R1L1Kidney R1L3Kidney R1L7Kidney
## ENSG00000146556 "ENSG00000146556" "0"        "0"        "0"       
## ENSG00000197194 "ENSG00000197194" "0"        "0"        "0"       
## ENSG00000197490 "ENSG00000197490" "0"        "0"        "0"       
## ENSG00000205292 "ENSG00000205292" "0"        "0"        "0"       
## ENSG00000177693 "ENSG00000177693" "0"        "0"        "0"       
## ENSG00000209338 "ENSG00000209338" "0"        "0"        "0"       
##                 R2L2Kidney R2L6Kidney
## ENSG00000146556 "0"        "0"       
## ENSG00000197194 "0"        "0"       
## ENSG00000197490 "0"        "0"       
## ENSG00000205292 "0"        "0"       
## ENSG00000177693 "0"        "0"       
## ENSG00000209338 "0"        "0"


layout(matrix(c(1,2,3,4,5,6), 3, 2, byrow=TRUE))
par(mar=c(2, 2, 2, 2))
DEGexp(geneExpMatrix1=geneExpMatrix1, geneCol1=1, expCol1=c(2,3,4,5,6), groupLabel1="kidney", geneExpMatrix2=geneExpMatrix2, geneCol2=1, expCol2=c(2,3,4,5,6), groupLabel2="liver", method="MARS" , output =  "DEGseq")


## Please wait...
## gene id column in geneExpMatrix1 for sample1:  1 
## expression value column(s) in geneExpMatrix1: 2 3 4 5 6 
## total number of reads uniquely mapped to genome obtained from sample1: 345504 354981 334557 366041 372895 
## gene id column in geneExpMatrix2 for sample2:  1 
## expression value column(s) in geneExpMatrix2: 2 3 4 5 6 
## total number of reads uniquely mapped to genome obtained from sample2: 274430 274486 264999 255041 284205 
## 
## method to identify differentially expressed genes:  MARS 
## pValue threshold: 0.001 
## output directory: none 
## 
## The outputDir is not specified! 
## Please wait ...
## Identifying differentially expressed genes ...
## Please wait patiently ...
## output ...
## The results can be observed in directory:  DEGseq

So when I open the output I only can see the value of genes in the two groups ("kidney and " "liver")

My question is there any way to view the value of the gene counts in each sample like kidney1, kidney2, kidney3

[Basti]

Your post is badly formatted, you should enhance the presentation. I do not understand your question because you created geneExpMatrix1 and geneExpMatrix2 which corresponds to the read counts and you are asking where you can view it

[ALOUSH ALI]

My question is about the output(differential gene expression analysis results) which contains results of logfoldchange and pvalues between the two groups (kidney and liver). So my question if there is a way to generate an output show those values between the samples among the groups like R1L1Kidney, R1L3Kidney, R1L7Kidney and liver1, liver2, liver3

[Basti]

logFC and p-values are results of a differential analysis between the groups, it does not exist in the context of individual samples