Difference between revisions of "Kevin's Assessment and Reflection"
From LMU BioDB 2013
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I compiled the raw data downloaded from array express | I compiled the raw data downloaded from array express | ||
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#[[Media:20131106_ArrayExpressADF_tATK_KM.adf.txt|Associated Data Files]] | #[[Media:20131106_ArrayExpressADF_tATK_KM.adf.txt|Associated Data Files]] | ||
#[[Media:20131106_ArrayExpressarraydesign_tATK_KM.txt|Array Design]] | #[[Media:20131106_ArrayExpressarraydesign_tATK_KM.txt|Array Design]] | ||
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#[[Media:20131106_ArrayExpresssdrf_tATK_KM.txt|Sample and Data Relationship]] | #[[Media:20131106_ArrayExpresssdrf_tATK_KM.txt|Sample and Data Relationship]] | ||
| − | into one excel file [[Media:20131119_teamATK_KM_compiledrawdata_(1)_(1).xls|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. [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae V. cholerae 1]] However, averages were performed first | + | into one excel file [[Media:20131119_teamATK_KM_compiledrawdata_(1)_(1).xls|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. [[http://www.openwetware.org/wiki/BIOL398-01/S10:Sample_Microarray_Analysis_Vibrio_cholerae 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. |
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| + | 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 [[http://www.openwetware.org/wiki/BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols V. cholerae 2]]. | ||
Revision as of 19:17, 12 December 2013
Statement of Work
I compiled the raw data downloaded from array express
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].
