Dear all,

I have a problem in understanding the contrast matrix in analyzing the
microarray data.

When slecting the differentially expressed gene in one case, I am using the
following contrast matrix

             S48-C48   S27-C27   bss-bsc   bts-btc
C48               0             0       0             0
S48               0             0       0             0
C27               0             0       0             0
S27                0             0       0              0
bsc                0             0      -1             0
bss                0             0       1              0
btc                 0             0       0             -1
bts                 0             0       0              1


when counted for coeff 3 and coeff 4, I am getting a set of gene as 60 for
coeff 3 and 58 for coeff 4

While using same data with the following contrast matrix

    bss-bsc bts-btc
bsc      -1       0
bss       1       0
btc       0      -1
bts       0       1

I am getting 580 for coeff 1 and 550 for coeff 2.

I am not able to understand what is the problem here as both the coeff i am
asking is same but still i get different results for two contrast matrix

Is something i am missing in understanding the principle of  making the
contrast.

Somebody please help in understanding the problem here, I shall be very
thankful for your kind help.

Best Wishes



-- 
Hemant Ritturaj Kushwaha

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