Dear list, I used averep function after normalization and before lmFit to average spot copies on microarrays. I noted that since a lot of spots have been averaged (the total number of spots have been reduced to 41000 from 43000), other spots do not have. See this example: Block Column Row ID Name Sequence ProbeUID GeneName logFC adj.P.Val B 1 85 183 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.266302 0.048228 0.181434 1 20 393 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB -0.20687 0.068295 -0.6233 1 56 294 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.110065 0.382405 -4.54642 1 22 299 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.085017 0.405978 -4.66767 1 53 457 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.080708 0.483304 -5.0517 1 17 39 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.063279 0.710629 -5.73913 1 45 199 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.051584 0.778778 -5.87993 1 64 279 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB -0.04158 0.800246 -5.91735 1 16 358 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.024847 0.880504 -6.03386 1 21 435 A_23_P135769 NM_001101 TTTAAAAACTGGAACGGTGAAGGTGACAGCAGTCGGTTGGAGCGAGCATCCCCCAAAGTT 2871 ACTB 0.000153 0.999438 -6.11393 1 4 111 A_23_P31323 NM_001101 ACTCTTCCAGCCTTCCTTCCTGGGCATGGAGTCCTGTGGCATCCACGAAACTACCTTCAA 8562 ACTB 0.283846 0.043577 0.472915 1 17 275 A_24_P226554 NM_001101 GCACCCAGCACAATGAAGATCAAGATCATTGCTCCTCCTGAGCGCAAGTACTCCGTGTGG 21338 ACTB 0.030637 0.848504 -5.9958 1 74 251 A_32_P137939 NM_001101 AGGCAGCCAGGGCTTACCTGTACACTGACTTGAGACCAGTTGAATAAAAGTGCGCACCTT 19564 ACTB -0.20387 0.177982 -2.87144 Why the group of first 10 probes was not averaged by avereps? Any suggestion will be appreciated. Thank you so much Erika [[alternative HTML version deleted]]