February 23, 2016

I think we are doing R-studio Check katherine's 2/16 notes. Get everything up to date by Spring Break.

"expected_count" in coding NOT "FPKM" or else we are re-normalizing previously normalized data.

Strategic clustering. #filtering to keep only those genes who mean expression is >10, play wiht this value to see how the size of toSearch changes. nothing is special about the number 10 myMeans <- apply(as.matrix(myCountData), 1, mean) toSearch <- myCountData[myMeans > 10 & !is.na9myMeans,]

we can differentiate between fed and non-fed with all of our knowledge. We need help with the geneontology search- search for function instead of just a transcription factor.

Keep in mind scientific goal: find genes that are differentially expressed between fed and non-fed and try to find candidates for genes that are at the beginning of the cascade.

we can coordinate with other organs group and see if we all converge on same gene from different approaches.

See where our work takes us, and then hunt down/research the genes we find.