Vkuehn Week 12

Week 12 Electronic Notebook

This week the GenMAPP users worked together to compile all of the raw data so that it would be ready to be analysed statistically and normalized.

The raw data that was taken from ArrayExpress was downloaded as a .txt file.
Then it was opened in Excel. The same was done with the Sample and Data Relationship File (sdrf.txt)
The ID od the chips was compared to each of the individual raw data chips. I was given L. major data files, and Kevin worked with L. infantum
The sdrf.txt file was rearranged so that all of the ones from each species were listed together. The irrelevant information was deleted from each sample, and only the characteristic descriptions and the names of the species were kept for each name. File:E-GEOD-10407.sdrf C.txt
We went through each of the raw data that corresponded to the name of the ID for both species and labeled the name with the last two digits of the ID in it. Then we deleted all of the irrelevant information. Only the name (now with the number in the header of the columns) and the expression ratio were kept.
These two columns were taken from each of the chip data files and all compiled onto one spreadsheet.
These were saved as Compiled Raw Data and the species followed by the species name. File:L.majorCompiledRawData.txt
The next step will be to take the data where the dyes were swapped and normalize those. Then we will need to try to link the data to the portions of the article.