problem extracting non AFE data with Agi4x44PreProcessing package
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@bernal-mizrachi-leon-2861
Last seen 8.1 years ago
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 ________________________________ This e-mail message (including any attachments) is for t...{{dropped:11}}
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