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The differentially methylated CpG islands were identified using the LIMMA package, as described for analysis of gene expression.
The resulting data were processed using the Illumina CASAVA package as described in version 1.6 of the CASAVA user guide.
All analyses were performed using BioConductor/R [54] and the stored procedures found in the exonmap package, as described in [14].
The study described here is part of the Nugo Proof of Principle study package as described by Baccini et al. [11].
Data analysis was performed in a R-software environment (freeware version 2.2.0) using the KTH package as described by Fitzimmons [17].
Survival analysis was carried out in R program using the 'survival' package as described previously.
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Data acquisition and analysis were performed using the Multielectrode MED64 hardware and software packages (Panasonic) essentially as described [7].
Viral packaging was performed as described.
In addition to this AMI that is capable of running on a single instance, we have also made available a second AMI EM-packages-in-the-Cloud-Node-v3.1 that provides users with the sAMI EM-packages-in-the-Cloud-Node-v3.1 thatut cAMI EM-packages-in-the-Cloud-Node-v3.1 thatple EC2 instAMI EM-packages-in-the-Cloud-Node-v3.1 that
Lentiviral and retroviral vectors were packaged as described [25], [28].
This construct was packaged as described for RT43.2GFP, transduced into PC12 cells, and G418-resistant cells selected by growth in medium containing 0.8 mg/ml G418.
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