[BioC] problem extracting non AFE data with Agi4x44PreProcessing package

[Bernal-Mizrachi, Leon]

I am trying to extract and old data done in 2006 on Scanner G2505B US23502303
and  was not extracted using Agilent Feature Extraction 9.1.3.1.

When I used Agi4x44PreProcessing package package, I found that my data does not
have in the features : Sequence, as needed in your package. I went to agilent and
downloaded the Sequence included in the platform.

The script goes:

targets=readTargets(file="targets.txt")

targets
                                              FileName
1  US23502303_251485027280_S01_GE1-v5_95_Feb07_1_1.txt
2  US23502303_251485027280_S01_GE1-v5_95_Feb07_1_2.txt
3  US23502303_251485027280_S01_GE1-v5_95_Feb07_1_3.txt
4  US23502303_251485027280_S01_GE1-v5_95_Feb07_1_4.txt
5  US23502303_251485027281_S01_GE1-v5_95_Feb07_1_1.txt
6  US23502303_251485027281_S01_GE1-v5_95_Feb07_1_2.txt
7  US23502303_251485027281_S01_GE1-v5_95_Feb07_1_3.txt
8  US23502303_251485027281_S01_GE1-v5_95_Feb07_1_4.txt
9  US23502303_251485027282_S01_GE1-v5_95_Feb07_1_1.txt
10 US23502303_251485027282_S01_GE1-v5_95_Feb07_1_2.txt
11 US23502303_251485027282_S01_GE1-v5_95_Feb07_1_3.txt
12 US23502303_251485027282_S01_GE1-v5_95_Feb07_1_4.txt
13 US23502303_251485027283_S01_GE1-v5_95_Feb07_1_1.txt
14 US23502303_251485027283_S01_GE1-v5_95_Feb07_1_2.txt
15 US23502303_251485027283_S01_GE1-v5_95_Feb07_1_3.txt
16 US23502303_251485027283_S01_GE1-v5_95_Feb07_1_4.txt
17 US23502303_251485027284_S01_GE1-v5_95_Feb07_1_1.txt
18 US23502303_251485027284_S01_GE1-v5_95_Feb07_1_2.txt
                    Treatment GErep Subject
1            KD OP5-1       1       a
2            KD OP5-2       1       b
3            KD OP5-3       1       c
4            KD OP0-1       2       a
5            KD OP0-2       2       b
6            KD OP0-3       2       c
7            ControlO3      3       a
8            ControlO3      3       b
9            ControlO3      3       c
10           KD DP5         4       a
11           KD DP5-2       4       b
12           KD DP5-3       4       c
13           KD DP0-1       5       a
14           KD DP0-2       5       b
15           KD DP0-3       5       c
16           ControlD1      6       a
17           ControlD2      6       b
18           ControlD3      6       c


> dd=read.AgilentFE(targets, makePLOT=FALSE)

Read US23502303_251485027280_S01_GE1-v5_95_Feb07_1_1.txt
Read US23502303_251485027280_S01_GE1-v5_95_Feb07_1_2.txt
Read US23502303_251485027280_S01_GE1-v5_95_Feb07_1_3.txt
Read US23502303_251485027280_S01_GE1-v5_95_Feb07_1_4.txt
Read US23502303_251485027281_S01_GE1-v5_95_Feb07_1_1.txt
Read US23502303_251485027281_S01_GE1-v5_95_Feb07_1_2.txt
Read US23502303_251485027281_S01_GE1-v5_95_Feb07_1_3.txt
Read US23502303_251485027281_S01_GE1-v5_95_Feb07_1_4.txt
Read US23502303_251485027282_S01_GE1-v5_95_Feb07_1_1.txt
Read US23502303_251485027282_S01_GE1-v5_95_Feb07_1_2.txt
Read US23502303_251485027282_S01_GE1-v5_95_Feb07_1_3.txt
Read US23502303_251485027282_S01_GE1-v5_95_Feb07_1_4.txt
Read US23502303_251485027283_S01_GE1-v5_95_Feb07_1_1.txt
Read US23502303_251485027283_S01_GE1-v5_95_Feb07_1_2.txt
Read US23502303_251485027283_S01_GE1-v5_95_Feb07_1_3.txt
Read US23502303_251485027283_S01_GE1-v5_95_Feb07_1_4.txt
Read US23502303_251485027284_S01_GE1-v5_95_Feb07_1_1.txt
Read US23502303_251485027284_S01_GE1-v5_95_Feb07_1_2.txt
Error in `[.data.frame`(ddaux$genes, , c(4, 6, 7, 8, 9, 10)) :
  undefined columns selected

Sorry to bother all of you. this may be a silly question but I have not been able
to overcome, this last part, any suggestions?

thanks all


Leon


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