Original dataset

We need now to create a new dataset which will include for each strain the two experiments, i.e the 3 replicates used to establish the nucleosome occupancy profile (NUC) and the 6 replicates from the H3K14 ChIP-CHIP experiment (ChIP). As you can see, the file Data/BY_S288c/Array/NucH3K14.conf contains the 3 .CEL previously used to infer the nucleosome occupancy and then come the 6 replicates for the ChIP-CHIP experiment.

$cat Data/BY_S288c/Array/NucH3K14.conf
CBY01   CBY01-II.CEL
CBY02   CBY02-I.CEL
CBY08   CBY08-II.CEL
BY02    BY02-I.CEL
BY07    BY07-I.CEL
BY10    BY10-I.CEL
BY14    BY14.CEL
BY16    BY16.CEL
BY17    BY17.CEL

So, let's extract and normalize the data from these nine .CEL files:

$NMcl2tab -c Data/BY_S288c/Array/NucH3K14.conf \
          -d Data/BY_S288c/Array/ -p S1/BY_S288c/BY_S288c.prb \
          -o Data/BY_S288c/Array/NucH3K14_norm.txt
          -n qql

And then use NMtdb to export the dataset into the binary format required by NucleoMiner (note that this time, the type attribute of the NMtdb configuration file, namely Data/BY_S288c/Array/NucH3K14.dbconf, is set to full, i.e that no pre-processing action is asked to NMtdb).

$cd Data/BY_S288c/Array/
$NMtdb -i NucH3K14_norm.txt -o NucH3K14_norm.db -c NucH3K14.dbconf