I have treated THP1 and AGS cells for 12, 24 and 48 hours with a bacterial toxin concentrations 0, 5, 10, 20, 40, and 80 ug/ml. Now I want to prove my results with statistical methods but I'm confused which one to use. Is it will be ANOVA post hoc test or simply t test. If it will be one tailed or two tailed, paired or unpaired.
As I understand, the cells were randomly distributed over the 6 different concentrations, but each cell was treated for 12, 24 and 48 hours. If this is correct, then you have a Between (6 levels of Concentration) x Within (3 levels of Time (hours)) design. First run a factorial repeated measures ANOVA. If the there are sign. effects (of Concentration, Time and/or the interaction) then you can run Post Hoc tests. Before running these tests, check the distributions of the measures on the treated cells with histograms. If they obviously do not look normal, then run a non-parametric test such as the f1.LD.f1 from the parLD R package (https://www.jstatsoft.org/article/view/v050i12 )
I suppose you normalize the images of the cells like in this stdudy: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1224512
As I understand, the cells were randomly distributed over the 6 different concentrations, but each cell was treated for 12, 24 and 48 hours. If this is correct, then you have a Between (6 levels of Concentration) x Within (3 levels of Time (hours)) design. First run a factorial repeated measures ANOVA. If the there are sign. effects (of Concentration, Time and/or the interaction) then you can run Post Hoc tests. Before running these tests, check the distributions of the measures on the treated cells with histograms. If they obviously do not look normal, then run a non-parametric test such as the f1.LD.f1 from the parLD R package (https://www.jstatsoft.org/article/view/v050i12 )
I suppose you normalize the images of the cells like in this stdudy: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1224512
to check statistical significance at different time intervals you can go head with repeated measures ANOVA (parametric test)/ Friedman's test (Non Parametric test) based on the fulfillment of the criteria for choosing the appropriate tests of significance.
Yes, ANOVA seems to fit well your data. But be careful when you enter factors values. They are values not "groups".
I mean : the software has to know that 12h is before 48h and furthermore that 48h=4*12h. The same for concentrations.
That's evidence, but I saw many people ignoring this evidence...
Moreover, I'm not sure that post hoc test would be really relevant. I would say that coefficient of the regression would help even more...
Regards
Yes it is dose and time dependent response. I have values in triplicates and after calculating mean I'm normalizing the data by subtracting with blank mean. Is it ok to use mean values or I should use normalized triplicate values for analysis. Thanks for valuable suggestions, Cyril Iaconelli , Jochen Wilhelm , Sujatha BK, Jos Feys
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