miRNA profile analysis

  • #1
114
11

Summary:

Hi there. I'm a PhD student learning how to interpret raw microarray data. I have selected a miRNA expression profile of mice liver tissue, of three groups: Control, High-fat diet(HFD) and HFD+drug.

Main Question or Discussion Point

microarry.png

Picture source:GSE94799

Following are the two different types of bar-digram that were observed. My questions are:
1. What do bars hanging below 0 mean in the first dig. ?
2. What do bars shooting from -6 mean, also why are they below 0?
3. Like a normal gene (non-ncRNA gene) expression profile where the expression level is measured by the logFC value, is F the parameter that is analogous to logFC here? Could you shed some light as how F works?
 

Answers and Replies

  • #2
jim mcnamara
Mentor
3,905
2,292
This is outside my field, so I googled for 'microarray data analysis' and found some tutorials. I would suggest starting there.

When I hit problems, in Grad school, that I did not understand my first stop was to check in with my advisor, have you done that?
 
  • #3
Ygggdrasil
Science Advisor
Insights Author
Gold Member
2019 Award
3,049
2,706
The y-axis of your graphs aren't labeled, so I don't think anyone can figure out what the values are supposed to mean. You'll probably need to consult the documentation from the program you used to obtain those graphs.

For logFC, this is short for the logarithm (usually base two) of the fold change of RNA abundance. For example, if the TPM of a gene A is 100 before treatment, and 200 after treatment, the fold change FC = 2 and log2(FC) = 1. Similarly for a gene that goes from 100 before treatment to 25 after treatment, FC = 0.25 and log2(FC) = -2.

In this context, I would assume that the F represented here refers to the F statistic for a statistical test such as ANOVA. The F is not directly related to log(FC), but is used to calculate the p-value.
 
  • Like
Likes SanjuktaGhosh and jim mcnamara
  • #4
114
11
Hi
I had googled but with narrower keywords, which displayed nothing relevant. I was attending a lousy workshop on (protein coding gene) microarray data analysis. So miRNA microarray analysis naturally came to my mind. The resource person could not answer my questions so I decided to post here.

No, I haven't checked it with my advisor yet.
Thanks
 

Related Threads on miRNA profile analysis

  • Last Post
Replies
2
Views
3K
  • Last Post
Replies
5
Views
2K
Replies
0
Views
696
Top