Difference between revisions of "Kevin's Assessment and Reflection"

Revision as of 19:24, 12 December 2013

Statement of Work

I compiled the raw data downloaded from array express

1. Associated Data Files
2. Array Design
3. Raw Data
4. Processed Data
5. Sample and Data Relationship

into one excel file 20131119_teamATK_KM_compiledrawdata.xls, log transformed the data, scaled and centered it, and ran Tstat and Pvalue calculations on the data as described in the V. cholerae instructions. V. cholerae 1 However, averages were performed first on the technical replicates corresponding to the same biological replicate, and then on each time period. Furthermore, Tstats and Pvalues were calculated by replicate rather than as one total calculation.

This data was imported into GenMAPP to create a gene database for S. pneumoniae, and color sets were created according to the instructions for V. cholerae V. cholerae 2. MAPPFinder was run, and a filtered ranked list was produced 20131210_tATK_filteredresults.xls. The sugar transmembrane transporter activity pathway was selected for further investigation, and a mapp of the genes in that pathway was produced using MAPPFinder 20131211_tATK_sugar_transmembrane_transporter_activity.mapp tATK jpeg MAPP. The function of each gene was determined based on the UniProt page for that particular gene, and a compiled list may be found here Media:Pathway_Gene_Info.xls. This information was incorporated into the report and presentation.