[BioC] Checking output of DESeq package analysis

[Anupreet kour [guest]]

I run DESeq package on my RNA seq hit count data (without replication). The input (hit count values) and output values (base means A & B) in the columns are the same. I want to make sure that these results are reliable as with a dataset of 78774 rows all the input values are the same as output values. I am getting fold changes and p-values which seems to be correct.  The code and outputs are given below:
(My code is running fine, my concern is output values (base mean A and B ) which are the same as WT_hit_counts  and Mutant_hit_counts)values. I think for some reason code is returning right p values but not the right base means. I will appreciate your help.

 -- output of sessionInfo(): 


> countsTable <- read.delim("filepath.txt", header=TRUE, stringsAsFactors=FALSE,row.names=1)

> conds <- factor(c("X", "Y"))

> head(countsTable)
             WT_hit_counts             Mutant_hit_counts
Gene 1                      1                      6
Gene 2                      9                     13
Gene 3                     10                     34
Gene 4                     34                     20
Gene 5                      2                      2
Gene 6                      8                     18
> cds3 <- newCountDataSet( countsTable, conds )

> cds3 <- estimateSizeFactors( cds3 )

> cds3 <- estimateDispersions( cds3, method="blind",sharingMode="fit-only")

> res <- nbinomTest(cds3,"X","Y")

> head(res)
id  baseMean baseMeanA baseMeanB foldChange log2FoldChange      pval padj
Gene 1   3.5         1         6  6.00   2.58 0.754    1
Gene 2  11.0         9        13  1.44   0.530 0.883    1
Gene 3  22.0        10        34  3.40   1.76 0.381   1
Gene 4 27.0        34        20  0.588    -0.76 0.67    1
Gene 5  2.0         2         2  1.00    0.00 1.00    1
Gene 6  13.0         8        18  2.25   1.16 0.67   1


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