Hi, I'm new into Affymetrix data evaluation and using Bioconductor, so sorry in advance for asking trivial questions. I was doing some testing with expresso and noticed something that I don't understand: my expresso command: eset <- expresso(Data, bg.correct=FALSE, normalize=FALSE, pmcorrect.method="pmonly", summary.method="avgdiff") This schould do no background correction, no normalization, summarize only perfect matches and calculate the average of them. Here's a small snippet from one of my cel files and the coressponding cdf file: cel file: [INTENSITY] NumberCells=285156 CellHeader=X Y MEAN STDV NPIXELS 237 61 183.3 31.3 36 237 62 292.5 52.0 36 238 61 196.0 20.0 36 238 62 243.0 74.2 36 239 61 88.5 15.7 36 239 62 94.3 12.2 36 240 61 93.3 13.9 36 240 62 82.3 11.8 36 241 61 128.3 18.7 36 241 62 134.0 18.4 36 242 61 116.3 16.7 36 242 62 101.5 20.6 36 243 61 113.8 22.0 36 243 62 127.5 16.8 36 244 61 296.5 39.3 36 244 62 146.3 19.5 36 245 61 116.5 19.8 36 245 62 112.3 18.7 36 246 61 81.3 11.0 36 246 62 82.0 12.2 36 247 61 159.3 23.1 36 247 62 92.8 13.6 36 248 61 122.8 19.3 36 248 62 134.8 21.4 36 249 61 316.3 37.1 36 249 62 1122.5 96.6 36 250 61 89.3 14.6 36 250 62 98.0 15.9 36 251 61 244.0 32.2 36 251 62 175.5 23.1 36 252 61 8075.8 1063.4 36 252 62 705.5 73.2 36 cdf file: [Unit1075_Block1] Name=A01157cds_s_at BlockNumber=1 NumAtoms=16 NumCells=32 StartPosition=0 StopPosition=15 CellHeader=X Y PROBE FEAT QUAL EXPOS POS CBASE PBASE TBASE ATOM INDEX CODONIND CODON REGIONTYPE REGION Cell1=237 61 N control A01157cds_s_at 0 13 T A T 0 32811 -1 -1 99 Cell2=237 62 N control A01157cds_s_at 0 13 T T T 0 33345 -1 -1 99 Cell3=238 62 N control A01157cds_s_at 1 13 A A A 1 33346 -1 -1 99 Cell4=238 61 N control A01157cds_s_at 1 13 A T A 1 32812 -1 -1 99 Cell5=239 61 N control A01157cds_s_at 2 13 T A T 2 32813 -1 -1 99 Cell6=239 62 N control A01157cds_s_at 2 13 T T T 2 33347 -1 -1 99 Cell7=240 62 N control A01157cds_s_at 3 13 A A A 3 33348 -1 -1 99 Cell8=240 61 N control A01157cds_s_at 3 13 A T A 3 32814 -1 -1 99 Cell9=241 61 N control A01157cds_s_at 4 13 G C G 4 32815 -1 -1 99 Cell10=241 62 N control A01157cds_s_at 4 13 G G G 4 33349 -1 -1 99 Cell11=242 62 N control A01157cds_s_at 5 13 A A A 5 33350 -1 -1 99 Cell12=242 61 N control A01157cds_s_at 5 13 A T A 5 32816 -1 -1 99 Cell13=243 62 N control A01157cds_s_at 6 13 C C C 6 33351 -1 -1 99 Cell14=243 61 N control A01157cds_s_at 6 13 C G C 6 32817 -1 -1 99 Cell15=244 62 N control A01157cds_s_at 7 13 A A A 7 33352 -1 -1 99 Cell16=244 61 N control A01157cds_s_at 7 13 A T A 7 32818 -1 -1 99 Cell17=245 61 N control A01157cds_s_at 8 13 G C G 8 32819 -1 -1 99 Cell18=245 62 N control A01157cds_s_at 8 13 G G G 8 33353 -1 -1 99 Cell19=246 61 N control A01157cds_s_at 9 13 T A T 9 32820 -1 -1 99 Cell20=246 62 N control A01157cds_s_at 9 13 T T T 9 33354 -1 -1 99 Cell21=247 61 N control A01157cds_s_at 10 13 G C G 10 32821 -1 -1 99 Cell22=247 62 N control A01157cds_s_at 10 13 G G G 10 33355 -1 -1 99 Cell23=248 61 N control A01157cds_s_at 11 13 G C G 11 32822 -1 -1 99 Cell24=248 62 N control A01157cds_s_at 11 13 G G G 11 33356 -1 -1 99 Cell25=249 62 N control A01157cds_s_at 12 13 C C C 12 33357 -1 -1 99 Cell26=249 61 N control A01157cds_s_at 12 13 C G C 12 32823 -1 -1 99 Cell27=250 62 N control A01157cds_s_at 13 13 C C C 13 33358 -1 -1 99 Cell28=250 61 N control A01157cds_s_at 13 13 C G C 13 32824 -1 -1 99 Cell29=251 61 N control A01157cds_s_at 14 13 G C G 14 32825 -1 -1 99 Cell30=251 62 N control A01157cds_s_at 14 13 G G G 14 33359 -1 -1 99 Cell31=252 62 N control A01157cds_s_at 15 13 C C C 15 33360 -1 -1 99 Cell32=252 61 N control A01157cds_s_at 15 13 C G C 15 32826 -1 -1 99 If I am doing the calculation by hand the result for A01157cds_s_at is 234.05, but expresso gives me 125.55. Am I doing something wrong or what's the reason behind this? Thanks in advance ... Cheers Marcus -- =================================================================== Marcus Albrecht Max-Planck-Institute for Molecular Genetics Department Lehrach Bioinformatics Group Harnackstrasse 23 e-mail: albrec_m@molgen.mpg.de 14195 Berlin Telephone: ++49 - (0)30 - 8413 1682