I am using 2 factor limma, factor1 3 groups, factor2 2 groups. It seems to be working fine, but I get results only for 2 groups of factor1, specifically Tables 1 and 2: factor1 gr1, factor2 gr1 vs. factor2 gr2, significant and non-sig.; Tables 3 and 4: factor1 gr2, factor2 gr1 vs. factor2 gr2, significant and non-sig; Tables 5 and 6: Difference significant and non-sig.; Table 7 significant and Table 8 non-sig. In each table I get statistics for the following: factor1gr1-factor2gr1 vs. factor1gr1-factor2gr2; factor1gr1-factor2gr1 vs. factor1gr2-factor2gr1; factor1gr1-factor2gr1 vs. factor1gr2-factor2gr2. It seems to be incomplete. Is it as it should be? What about factor1 group 3? What to do about it? -- Thanks in advance! / Jaroslav
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