Im trying to find the average A values for replicate chips after using the lmFit function. I can easily identify the average M values for each group of replicates, but I dont see a similar listing for the A values. I only appear to be generating one average A value for all replicates. Does the lmFit function do this, or am I doing something wrong... thanks Simon. > design <- designMatrix(targets, ref="Normal Pool") Found unique target names: AD 4 Normal Pool AD 21 AD 28 AD 34 AD 35 AD 45 AD 63 AD 65 AD 66 AD 70 AD 107 > fit <- lmFit(MA, design) > fit An object of class "MArrayLM" $coefficients #the M average of the technical replicates for each sample# AD 4 AD 21 AD 28 AD 34 AD 35 AD 45 [1,] -0.29077587 -0.33120458 0.05493782 0.002216203 -0.02790125 -0.23071666 [2,] 0.03370502 0.06603841 -0.11291981 0.151881419 -0.20978938 0.06414161 [3,] 0.17063392 -0.10746990 -0.17197063 0.011231556 -0.15972561 -0.08339154 [4,] -0.34079507 -0.02360503 0.20886973 -0.283838031 -0.34157942 0.13088139 [5,] -0.20889418 -0.08203535 -0.19620931 0.290167793 -0.45876852 0.04305072 AD 63 AD 65 AD 66 AD 70 AD 107 [1,] 0.29659220 0.029823487 0.15005839 -0.529235510 0.089936386 [2,] -0.11305790 -0.262700172 0.11602458 0.154556727 -0.006538595 [3,] 0.04773510 -0.125797143 0.10295488 0.219021314 0.098044781 [4,] -0.09582606 -0.005583817 -0.10466737 0.002683542 0.077066385 [5,] -0.01504539 -0.025666728 -0.06597346 0.234770549 -0.089887749 25083 more rows ... $Amean #why isnt the format the same as for M?, there only appears to be one set of A values# [1] 10.967244 15.627646 15.384239 7.634115 12.521264 25083 more elements ... -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1873 bytes Desc: not available Url : https://www.stat.math.ethz.ch/pipermail/bioconductor/attachments /20040111/b50e2f3b/attachment.bin

The Amean values are intended to give an idea of the overall expression level for each gene. The A-values are not used to analyze differential expression and therefore there is usually no purpose is fitting a linear model to them, which is what would give you the same output format as the M-values. If you want to see the mean A-values corresponding to the M-values for each group, you could simply use fitA <- lmFit(MA$A, design) and look in fitA$coef. Note this only works when the design matrix is a simple indicator matrix for the RNA groups as in your example. There are no plans to specially support this sort of analysis in limma. Gordon > Im trying to find the average A values for replicate chips after using > the lmFit function. I can easily identify the average M values for each > group of replicates, but I dont see a similar listing for the A values. > I only appear to be generating one average A value for all replicates. > Does the lmFit function do this, or am I doing something wrong... > > thanks > Simon. ... > $Amean #why isnt the format the same as for M?, there only appears to > be one set of A values# > [1] 10.967244 15.627646 15.384239 7.634115 12.521264 > 25083 more elements ...