fit<- lmFit(signals,design, method = 'robust') There were 50 or more warnings (use warnings() to see the first 50) > warnings() Warning messages: 1: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 2: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 3: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 4: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 5: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 6: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 7: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 8: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 9: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 10: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 11: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 12: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 13: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 14: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 15: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 16: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 17: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 18: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 19: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 20: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 21: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 22: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 23: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 24: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 25: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 26: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 27: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 28: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 29: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 30: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 31: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 32: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 33: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 34: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 35: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 36: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 37: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 38: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 39: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 40: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 41: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 42: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 43: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 44: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 45: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 46: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 47: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 48: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 49: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps 50: In rlm.default(x = X, y = y, weights = w, ...) : 'rlm' failed to converge in 20 steps I dont understand why i am having this warnings from lmFit (). Can i just ignore and continue further with analysis or do i have to fix it to get the correct analysis done? I have also tried weighing them (which could be wrong) but results the same >arrayWeights(norm_exprs, design=design, weights = NULL, method = "genebygene", maxiter = 50, tol = 1e-10, trace=FALSE) Please help me with this. > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-apple-darwin13.1.0 (64-bit) locale: [1] sv_SE.UTF-8/sv_SE.UTF-8/sv_SE.UTF-8/C/sv_SE.UTF-8/sv_SE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] MASS_7.3-33 limma_3.20.6 oligoClasses_1.26.0 BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affyio_1.32.0 Biobase_2.24.0 BiocGenerics_0.10.0 Biostrings_2.32.0 bit_1.1-12 codetools_0.2-8 ff_2.2-13 [8] foreach_1.4.2 GenomeInfoDb_1.0.2 GenomicRanges_1.16.3 IRanges_1.22.9 iterators_1.0.7 parallel_3.1.0 stats4_3.1.0 [15] tools_3.1.0 XVector_0.4.0 zlibbioc_1.10.0 Best Nikul -- सर्वेsत्र सुखिन: सन्तु सर्वे सन्तु निरामया: | सर्वे भद्राणि पश्यन्तु मा कश्चित दु:ख माप्नुयात || [[alternative HTML version deleted]]