Hello, I have phenotypic expression score data from 1 hit, 2 hit and control genes in flies. I have been asked to do some kind of visualization with R using this data. However, since the data has very few parameters i.e. just gene hit names and scores I have been unable to use ggplot, qplot or other such packages in R effectively with it. I have only been able to make basic visualization plots with the data. I need help to find a suitable analysis pipeline using R for this data or some other kind of analysis pipeline that will help me to get useful results from it and also find possible convergence from these in humans (maybe by using GO). If anyone has experience using such data please enlighten me about the steps you followed or link me to more articles/ papers showing analysis of such data as I couldn't find much help on the internet. Thank you for your suggestions.
Could you give us a few rows of the data that you have?
w1118/GMR-Gal4 106488,GMR 106488,GMR/(PAK)kk
17.31798313 30.36516372 29.29103696
19.70175042 32.53293186 34.03868551
18.5845783 35.86677539 35.14690498
This is a sample of the data. It is the qPCR score in female crosses, and the 1st two columns were used as controls for the remaining genes. Thanks.
What question(s) are you trying to address ? What do you consider a useful result ? What's the data and where is it coming from ?
It's qPCR data. And by useful I mean a graph or a non-parametric test that can give some valuable insight into the phenotypic expression level of the genes, or a GO study that can show convergence between the orthologs. The aim of the project is to find the change in expression level due to mutation and to establish correlation between these affected genes in flies and humans.