What Insights Can Be Gained from MiRNA Profile Bar Diagrams in GSE94799?

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Discussion Overview

The discussion revolves around the interpretation of miRNA profile bar diagrams from the dataset GSE94799. Participants are exploring the meaning of specific values represented in the diagrams, particularly those below zero, and the relationship between different statistical measures used in the analysis.

Discussion Character

  • Exploratory
  • Technical explanation
  • Debate/contested

Main Points Raised

  • One participant questions the significance of bars hanging below zero in the first diagram and seeks clarification on their meaning.
  • Another participant asks about bars shooting from -6 and why they are below zero.
  • A participant draws a parallel between the parameter F in the context of miRNA analysis and logFC in gene expression profiles, suggesting that F may refer to the F statistic from statistical tests like ANOVA.
  • Concerns are raised about the lack of y-axis labeling in the graphs, which complicates the interpretation of the values.
  • One participant shares their experience of seeking resources and tutorials on microarray data analysis, indicating a lack of relevant information found through narrower searches.

Areas of Agreement / Disagreement

Participants express uncertainty regarding the interpretation of the bar diagrams and the statistical measures involved. There is no consensus on the meanings of the values below zero or the relationship between F and logFC.

Contextual Notes

The discussion highlights limitations such as the absence of labeled axes in the graphs and the need for further clarification on the statistical parameters used in the analysis.

Who May Find This Useful

Researchers or students interested in miRNA analysis, microarray data interpretation, and statistical methods in biological data analysis may find this discussion relevant.

TytoAlba95
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TL;DR
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.
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?
 
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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?
 
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.
 
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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
 

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