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How package I use for verify differentialy expressed genes after Normalization with marrayNorm?

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Marcelo Luiz de Laia ▴ 770

@marcelo-luiz-de-laia-377

Last seen 10.2 years ago

Hi All, I was normalized my cDNA macroarrays with marrayNorm. Now, I have a marrayNorm object ka.susc.norm and I would like to verify if exist differentialy genes expressed. How package I use for this? Another question: I put the Control in the Green (Cy3) and the Treated in the Red (Cy5). Is it ok? Any comments and suggestions are very appreciated! Thanks. Marcelo Luiz de Laia, M.Sc. Dep. de Tecnologia, Lab. Bioqu?mica e de Biologia Molecular Universidade Estadual Paulista - UNESP Via de Acesso Prof. Paulo Donato Castelane, Km 05 14.884-900 - Jaboticabal, SP, Brazil PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.) Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia@yahoo.com ---

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ADD COMMENT • link updated 21.1 years ago by Jean Yee Hwa Yang ▴ 920 • written 21.1 years ago by Marcelo Luiz de Laia ▴ 770

score 0 · Answer 1 · 2003-11-03

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Jean Yee Hwa Yang ▴ 920

@jean-yee-hwa-yang-104

Last seen 10.2 years ago

Hi Marcelo, Use the package limma, take a look at the help file for the function "lmFit"; help(lmFit) for more information. > I put the Control in the Green (Cy3) and the Treated in the Red (Cy5). Is it > ok? That is fine, maM(ka.susc.norm) will return normalized log-ratios = log(Cy5 / cy3) which is log(Treated/control). Cheers Jean

ADD COMMENT • link 21.1 years ago Jean Yee Hwa Yang ▴ 920

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Thanks Jean. > -----Original Message----- > From: Jean Yee Hwa Yang [mailto:jean@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. ---

ADD REPLY • link 21.1 years ago Marcelo Luiz de Laia ▴ 770