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2 hours ago by

pune, India

I downloaded Agilent 2 color data of Agilent_sure-print_g3_ge_8x60k platform and performed differential Expression I followed pipeline given here. Now I want to further analyze it using WGCNA. After normalization by normalizeWithinArrays, the data is transformed to MAlist. There are Two matrix in the MA list. First is M matrix that contains log2 expression values and second is A matrix that contains average log2 expression values. My question is which values should be considered for further analysis?
The MA list object looks like :

An object of class "MAList" $targets
Sample names
1
2

$genes Row Col ControlType ProbeName SystematicName 1 1 1
1 GE_BrightCorner GE_BrightCorner 2 1 2 1
DarkCorner DarkCorner 3 1 3 1 DarkCorner
DarkCorner 4 1 4 0 A_23_P326296 NM_144987 5 1
5 0 A_24_P287941 NM_013290 62971 more rows ...

$source [1] "agilent"

$printer $ngrid.r [1] 1

$ngrid.c [1] 1

$nspot.r [1] 384

$nspot.c [1] 164

$M
Sample 1 Sample2 [1,] 0.6499983
0.5357494 [2,] 0.1989391 -0.1607216 [3,] -0.1824825 -0.6443034 [4,] -0.9675712 -1.8801010 [5,] 0.4388240 1.0480026
62971 more rows ...

$A

Sample 1                                                      Sample 2
  

[1,] 14.565923
14.605850 [2,] 2.897886 3.441465 [3,] 3.408228 3.090076 [4,] 6.348938 6.201913 [5,] 7.635765 6.971435
62971 more rows ...

Thank you

Parin

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modified 2 hours ago

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2 hours ago
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parinv10



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