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 04-26-2011, 03:09 PM #1 lei Member   Location: germany Join Date: Mar 2010 Posts: 14 a question about Saturation analysis in MEDIPS hi, I am now using MEDIPS for MCIP-seq analysis. For the Saturation analysis, I don't know how to explain the results. So which value I should focuse in order to answer the question that how many reads is sufficient for further analysises? for example, here are the results for two samples, how to know whether the reads number is enough or not. sample 1: \$distinctSets [,1] [,2] [1,] 0 0.0000000 [2,] 421516 0.4890383 [3,] 843032 0.6566207 [4,] 1264548 0.7414630 [5,] 1686064 0.7923945 [6,] 2107580 0.8271925 [7,] 2529096 0.8514569 [8,] 2950612 0.8699040 [9,] 3372128 0.8844299 [10,] 3793644 0.8959736 [11,] 4215166 0.9053887 \$estimation [,1] [,2] [1,] 0 0.0000000 [2,] 421516 0.4972269 [3,] 843032 0.6631622 [4,] 1264548 0.7467590 [5,] 1686064 0.7974522 [6,] 2107580 0.8311024 [7,] 2529096 0.8552331 [8,] 2950612 0.8731673 [9,] 3372128 0.8873165 [10,] 3793644 0.8985876 [11,] 4215160 0.9077852 [12,] 4636676 0.9153314 [13,] 5058192 0.9218284 [14,] 5479708 0.9274455 [15,] 5901224 0.9323282 [16,] 6322740 0.9365573 [17,] 6744256 0.9402298 [18,] 7165772 0.9434950 [19,] 7587288 0.9465256 [20,] 8008804 0.9491727 [21,] 8430333 0.9516126 \$numberReads [1] 8430333 \$maxEstCor [1] 8.430333e+06 9.516126e-01 \$maxTruCor [1] 4.215166e+06 9.053887e-01 sample 2: \$distinctSets [,1] [,2] [1,] 0 0.0000000 [2,] 677985 0.6015521 [3,] 1355970 0.7518315 [4,] 2033955 0.8192142 [5,] 2711940 0.8577985 [6,] 3389925 0.8830463 [7,] 4067910 0.9005583 [8,] 4745895 0.9136279 [9,] 5423880 0.9235792 [10,] 6101865 0.9314847 [11,] 6779856 0.9379848 \$estimation [,1] [,2] [1,] 0 0.0000000 [2,] 677985 0.6054022 [3,] 1355970 0.7542983 [4,] 2033955 0.8216820 [5,] 2711940 0.8597790 [6,] 3389925 0.8845496 [7,] 4067910 0.9017873 [8,] 4745895 0.9148084 [9,] 5423880 0.9246916 [10,] 6101865 0.9325375 [11,] 6779850 0.9387990 [12,] 7457835 0.9440903 [13,] 8135820 0.9485184 [14,] 8813805 0.9523514 [15,] 9491790 0.9555902 [16,] 10169775 0.9585080 [17,] 10847760 0.9609586 [18,] 11525745 0.9631440 [19,] 12203730 0.9651430 [20,] 12881715 0.9669121 [21,] 13559713 0.9684958 \$numberReads [1] 13559713 \$maxEstCor [1] 1.355971e+07 9.684958e-01 \$maxTruCor [1] 6.779856e+06 9.379848e-01 Thanks for your help!