A total of 374 CEL files of samples from platform GPL1320 were used to construct the network and involved three treatment types (biotic stress, development, abiotic stress) and 13 series.
With the exception of a guitar part recorded for "Slow Jam", he composed the music exclusively from a file of samples he had assembled over several years.
For example, we would name the Material file of samples LAB-1 and LAB-2 as m_LAB-1.txt and m_LAB-2.txt, respectively.
We downloaded raw data (CEL files) of each sample, controlled and removed low quality samples using affy [ 26] and affyQCReport [ 27] packages, and finally retained 86 GSE datasets involving 4403 samples for 89 diseases (Additional file 1).
Table S4 lists the GEO accession number for the Cel files of each sample.
No reads from filtered BAM files of any sample map onto the combined bacterial reference.
Strand-specific bedgraph files of each sample were imported into IGV along with the W303_ALAV0000000.gff file as the reference.
The adaptors and unique tag regions were trimmed by Mothur, following the 454 SOP (http://www.mothur.org/wiki/454_SOP) to get fasta-format files of each sample.
For our testing, we modified the firmware and implemented a procedure for capturing arbitrarily long files of received samples at the full 100 MS/s rate.
Cell files of six samples were normalized and analyzed in Partek Genomics Suite Software.
