[BioC] DESeq cuont table normalization

[Fatemehsadat Seyednasrollah]

Hello,

I am following the DESeq vignette and repeating what is mentioned there for my dataset. 
There is a step in the vignette which tries to normalize the count table to gain a common scale :
> head( counts( cds, normalized=TRUE ) )

When I run this line and then agin run the command : 
head(counts(cds))

I see the amount of reads before normalization. Should not it change to the new amounts I mean the normalized amounts?


> print (head(counts(mine, normalized = TRUE)))
                  X3        X5          X4       X4.1        X2       X3.1
A1BG     186.0036964 96.798204 231.6504223 90.4352020 92.027309  40.852657
A1BG-AS1  22.3204436 29.143545  15.0666941 28.3718281 18.191445   8.881012
A1CF       0.9300185  1.040841   0.9416684  1.7732393  1.070085   0.000000
A2LD1     93.0018482 73.899704  92.2835016 86.0021039 63.135014 113.676959
A2M        4.6500924  5.204205  21.6583728  0.8866196  5.350425   5.328607
A2ML1      0.0000000  0.000000   0.0000000  0.0000000  0.000000   1.776202
                X1       X1.1
A1BG      66.40690  90.562533
A1BG-AS1  21.75399  14.916182
A1CF       0.00000   1.065442
A2LD1    100.75530 121.460339
A2M       11.44947   5.327208
A2ML1      0.00000   0.000000


> head(counts(mine))
          X3 X5  X4 X4.1 X2 X3.1 X1 X1.1
A1BG     200 93 246  102 86   46 58   85
A1BG-AS1  24 28  16   32 17   10 19   14
A1CF       1  1   1    2  1    0  0    1
A2LD1    100 71  98   97 59  128 88  114
A2M        5  5  23    1  5    6 10    5
A2ML1      0  0   0    0  0    2  0    0