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Several important large-scale datasets have been produced recently that will be incorporated into TGD Wiki.
Large-scale datasets have been produced for yeast [ 3, 23] and E. coli [ 24, 25].
Several datasets have been produced by applying event extraction tools to biomedical literature (e.g. BioContext [ 29], EVEX [ 22]).
These datasets have been produced using Affymetrix arrays and are available at the NCBI Gene Expression Omnibus GEOO) data repository under Accession number GSE24465.
These datasets have been produced using Codelink BioArrays and are available at the ArrayExpress data repository under Accession number E-MEXP-861.
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In contrast, the South African generic drugs in the dataset have been produced pursuant to voluntary license agreements with brand companies.
A dataset has been produced including both ESA CS2 IPF Baseline B SSH and the SSH series coming from this study.
One is that it can be tricky to ensure reproducibility of analyses; or rather, the onus is completely on the individuals who are using the script to document in some way the datasets that have been produced.
The fact that Pyicos performs well with simulated replicated data presents the advantage of making possible to analyse many of the published datasets that have been produced without replica.
The automated identification of suitable reference genes by the use of tools such as RefGenes [ 30] might be useful, taking care to focus on functionally unrelated candidates, provided that transcriptomic data that are targeted by this tool are generalised to all published datasets, including those that have been produced from filamentous fungi.
This microarray platform expansion has hindered the direct comparison between numerous datasets of a given phenotype that have been produced using several generations of arrays.
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