One of the projects I am working on contains IHC. Now that the staining is done as well as the scoring (Semi quantitative), I was wondering which is the best way to present those results? Using the median value does not represent in some cases the truth, whereas I am not sure if I can use an average value of the scores I have.
Which is the best statistical method to analyze the significance of those results?
You have to transform the images into a digital data (Numbers)
Percentage of the Color
Optical Density
Number of positive cells to negative ones
You have to have a reference from pubmed to help you to identify the statistics on the tissues you are using.
It really depends on what marker are you using, and the objective of your work. Are you evaluating intensity of the stain? just presence? hotspots?
Did you have any reliable internal control? Sometimes, a good fluorescence microscope comes with a software that helps in determining the mean pixel density count of the protein (in this case your protein of interest) and in comparing that one with pixel density of internal control (DAPI, MAP2 etc). The ratio of the two will give you a number and you can plot a graph based on those numbers and see if that gives an idea whether the specific protein is higher or lower compared to the internal control.
Hope it helps.
Thank you all for the answers suggested to me and sorry for not replying sooner than now. we have already used a semi-quantitative algorithm to give each different sample stained a score, in which the cell percentage stained was taken into consideration as well as the staining intensity in those cells. This way each sample now has its own "score".
As these samples are devided into two groups, is it right to use an average of these scores for each group to give a general view of the stainings? or maybe some other method, like median for example? or maybe something different that we didn't think of.
This is my problem for the time being. And thank you all once again for the interrest.
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