[BioC] How package I use for verify differentialy expressed genes
after Normalization with marrayNorm?
Marcelo Luiz de Laia
mlaia at fcav.unesp.br
Mon Nov 3 22:20:13 MET 2003
Thanks Jean.
> -----Original Message-----
> From: Jean Yee Hwa Yang [mailto:jean at biostat.ucsf.edu]
(...)
> That is fine, maM(ka.susc.norm) will return normalized log-ratios =
> log(Cy5 / cy3) which is log(Treated/control).
Hummm! When I typed maM(ka.susc.norm) I see a matrix with 4 colunms x 7680
rows. (Please, see it below).
But, my genes are duplicated in the nylon filter membrane!
Then, I should have only the half (3840 genes).
Which will my error be?
Thanks
Marcelo
++++++++++++
maM(ka.susc.norm) return
Susc_01.dats Susc_02.dats Susc_03.dats
[1,] -0.4164532 -0.6577436 NA
[2,] 6.0630024 2.1253564 -0.8368827
[3,] 3.7762845 1.6976429 -1.2527906
(...)
[10,] NA NA NA
(...)
[7678,] 2.7573818 3.3141e+00 0.6502689
[7679,] NA NA NA
[7680,] NA NA NA
The last two rows is Zero(0), because it is blank (spoted water without
DNA). I have 530 blanks in my array.
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