[BioC] Question about excluding Affymetrix spike controls from normalization

[Tan, MinHan]

Good evening,
 
Apologies for the long genelist that follows the text.
 
I have a question about data analysis - I am hoping to exclude the
bacterial spike in control results from rma normalization (or change all
corresponding gene values to the same result). (I have included the list
below) The problem arose because Affymetrix recently introduced the
Ambion spike in control kit - some experiments included these spike-ins,
while others did not.
 
How can I manipulate the Affybatch object following readAffy, and before
rma normalization, to convert all the results of these genes to the same
value in all the arrays? Alternatively, would it make sense to work on
all AFFX genes altogether? 
 
Thank you!
 
Regards,
Min-Han Tan
 
 
 
 
 
AFFX-DapX-5_at 986.2 P 0.000060 L38424 B subtilis dapB, jojF, jojG genes
corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-M_at 1600.9 P 0.000754 L38424 B subtilis dapB, jojF, jojG
genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3
represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-DapX-3_at 1731.7 P 0.000070 L38424 B subtilis dapB, jojF, jojG
genes corresponding to nucleotides 1358-3197 of L38424 (-5, -M, -3
represent transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-LysX-5_at 159.9 P 0.001248 X17013 B subtilis lys gene for
diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of
X17013  (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3
prime respectively)
AFFX-LysX-M_at 244.2 A 0.067678 X17013 B subtilis lys gene for
diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of
X17013  (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3
prime respectively)
AFFX-LysX-3_at 340.0 P 0.000044 X17013 B subtilis lys gene for
diaminopimelate decarboxylase corresponding to nucleotides 350-1345 of
X17013  (-5, -M, -3 represent transcript regions 5 prime, Middle, and 3
prime respectively)
AFFX-PheX-5_at 185.8 P 0.000446 M24537B subtilis pheB, pheA genes
corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-M_at 225.9 P 0.004484 M24537B subtilis pheB, pheA genes
corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-PheX-3_at 286.8 P 0.001410 M24537B subtilis pheB, pheA genes
corresponding to nucleotides 2017-3334 of M24537 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-5_at 239.3 P 0.002556 X04603 B subtilis thrC, thrB genes
corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-M_at 327.8 P 0.000147 X04603 B subtilis thrC, thrB genes
corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-ThrX-3_at 471.2 P 0.000509 X04603 B subtilis thrC, thrB genes
corresponding to nucleotides 248-2229 of X04603 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-TrpnX-5_at 36.8 A 0.089478 K01391 B subtilis TrpE protein, TrpD
protein, TrpC protein corresponding to nucleotides 1883-4400 of K01391
(-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime
respectively)
AFFX-TrpnX-M_at 6.4 A 0.814869 K01391 B subtilis TrpE protein, TrpD
protein, TrpC protein corresponding to nucleotides 1883-4400 of K01391
(-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime
respectively)
AFFX-TrpnX-3_at 16.1 A 0.588620 K01391 B subtilis TrpE protein, TrpD
protein, TrpC protein corresponding to nucleotides 1883-4400 of K01391
(-5, -M, -3 represent transcript regions 5 prime, Middle, and 3 prime
respectively)
AFFX-r2-Bs-dap-5_at 875.4 P 0.000244 Bacillus subtilis /REF=L38424
/DEF=B subtilis dapB, jojF, jojG genes corresponding to nucleotides
1439-1846 of L38424 /LEN=1931 (-5, -M, -3 represent transcript regions 5
prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-dap-M_at 1732.7 P 0.000244 Bacillus subtilis /REF=L38424
/DEF=B subtilis dapB, jojF, jojG genes corresponding to nucleotides
2055-2578 of L38424 /LEN=1931 (-5, -M, -3 represent transcript regions 5
prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-dap-3_at 2512.5 P 0.000244 Bacillus subtilis /REF=L38424
/DEF=B subtilis dapB, jojF, jojG genes corresponding to nucleotides
2634-3089 of L38424 /LEN=1931 (-5, -M, -3 represent transcript regions 5
prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-lys-5_at 185.1 P 0.000244 Bacillus subtilis /REF=X17013
/DEF=B subtilis lys gene for diaminopimelate decarboxylase corresponding
to nucleotides 411-659 of X17013 /LEN=1108 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-lys-M_at 164.7 P 0.000244 Bacillus subtilis /REF=X17013
/DEF=B subtilis lys gene for diaminopimelate decarboxylase corresponding
to nucleotides 673-1002 of X17013 /LEN=1108 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-lys-3_at 241.6 P 0.000732 Bacillus subtilis /REF=X17013
/DEF=B subtilis lys gene for diaminopimelate decarboxylase corresponding
to nucleotides 1008-1263 of X17013 /LEN=1108 (-5, -M, -3 represent
transcript regions 5 prime, Middle, and 3 prime respectively)
AFFX-r2-Bs-phe-5_at 287.1 P 0.000244 Bacillus subtilis /REF=M24537
/DEF=B subtilis pheB, pheA genes corresponding to nucleotides 2116-2382
of M24537 /LEN=1409 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
AFFX-r2-Bs-phe-M_at 327.5 P 0.000732 Bacillus subtilis /REF=M24537
/DEF=B subtilis pheB, pheA genes corresponding to nucleotides 2484-2875
of M24537 /LEN=1409 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
AFFX-r2-Bs-phe-3_at 457.0 P 0.000244 Bacillus subtilis /REF=M24537
/DEF=B subtilis pheB, pheA genes corresponding to nucleotides 2897-3200
of M24537 /LEN=1409 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
AFFX-r2-Bs-thr-3_s_at 674.7 P 0.023926 Bacillus subtilis /REF=X04603
/DEF=B subtilis thrC, thrB genes corresponding to nucleotides 1689-2151
of X04603 /LEN=2073 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
AFFX-r2-Bs-thr-M_s_at 662.1 P 0.001953 Bacillus subtilis /REF=X04603
/DEF=B subtilis thrC, thrB genes corresponding to nucleotides 995-1562
of X04603 /LEN=2073 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
AFFX-r2-Bs-thr-5_s_at 366.3 P 0.000244 Bacillus subtilis /REF=X04603
/DEF=B subtilis thrC, thrB genes corresponding to nucleotides 288-932 of
X04603 /LEN=2073 (-5, -M, -3 represent transcript regions 5 prime,
Middle, and 3 prime respectively)
 

This email message, including any attachments, is for the so...{{dropped}}