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I am doing a gene expression analysis on blood samples collected from the same 8 goats. My sampling points are before LPS-treatment (0h), and 1h, 2h, 5h and 24h after treatment. I want to compare the mean expression of each post-treatment to the before-treatment values. Due to problems in RNA-extraction, one sample is missing at 1h and one sample is missing at 2h. Is it possible to do a paired t-test with unequal sample size? E.g n=8 at 0h and n=7 at 1h/2h?

I'm using log2 transformed data for the statistical analysis. (We are have decided not to correct for multiple comparisons, but we use a fold-change limit instead)

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You can not do a t-test for paired data with unequal sample-sizes but you can omit cases with missing data for the analysis of these times: Do a n=8 comparison for 5h an 24 h and an n=7 comparison for n=1h an n=2h.

Have you considered repeated-measurements-ANOVA instead of all those t-tests? With n so small and 4 different tests, alpha Inflation is an issue to be considered.

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