Teamname Week 15 Status Report

Miles Malefyt

What worked?

• This week I finally began to see the fruits of my labor over the past couple weeks. I successfully uploaded some data to GenMAPP even though some of it didnt work, it turns out that a lot of the gene IDs went through. The test file I used was the t15 log fold change. I also went through and re-did some of the original title heading in the xls file before I converted it into a text file and compiled in on GenMAPP

What didn't work?

• There was an issue with a lot of the gene IDs that GenMAPP didnt recognize their format. Also, before I corrected it the names of the columns weren't importing into GenMAPP

What will I do next to fix what didn't work?

• Well first we need to isolate the problem. There seems to be 3 sets of IDs for each replicate and 3 replicates. I suspect that it has something to do with the labeling they gave the genes to distinguish the two megaplasmids and the chromosome. If I am correct then I will have to talk to the coder to see what we can do about it. If its another error then we will have to get to the bottom of that.

Lauren Magee: Reflection Questions

1. What worked?
   • A lot has been accomplished since the last status report and I now have a file that is ready for the GenMapp protocol. I have been going through an intense editing process of this file for sometime now with Dr. Dahlquist and my fellow group members, so that the file I currently have will hopefully produce error free results during GenMapp analysis.
2. What didn't work?
   • In my original data file for GenMapp, I had accidentally copied over an entire column, but had labeled it as something else. This made the rest of my calculations, that had been based off of this data, invalid so I had to carefully correct my mistakes. If this error hadn't been pointed out by Dr. Dahlquis during the editing process, the results for my entire GenMapp analysis would have been incorrect. That is why professor and peer review is so important, because they are able to catch mistakes you may have glazed over in your own editing.
3. What will I do next to fix what didn't work?
   • I have already fixed the incorrect column in my original data set, so I know have an error free document to run in GenMapp. There may be new errors that are shown while I am following the GenMapp protocol, but for now, everything appears correct.