I am analyzing 12 Agilent slides with LIMMA (ver 1.7.7, R: 1.9.1) I load my targets file with this line... targets<-readTargets(file="targets.txt", path = "C:/Documents and Settings/giovanni/analysis") ... and I read the data with this line: RG <-read.maimages(name=targets$Name,source="agilent", ext="txt", path = "C:/Documents and Settings/giovanni/analysis/data",verbose=TRUE, wt.fun=mywtfun(c(1))) Now, if I type 'targets' I obtain (as expected) the following: slide.number Name FileName cy5 cy3 jc_251197823988_S01_A01 1 e6-c3h jc_251197823988_S01_A01.txt e c jc_16011978013880_S01_A01 2 c3-e6h jc_16011978013880_S01_A01.txt c e jc_16011978013882_S01_A01 3 e4-c7h jc_16011978013882_S01_A01.txt e c jc_16011978013881_S01_A01 4 c7-e4h jc_16011978013881_S01_A01.txt c e jc_251197823979_S01_A01 5 e7-c8h jc_251197823979_S01_A01.txt e c jc_251197823980_S01_A01 6 c8-e7h jc_251197823980_S01_A01.txt c e jc_251197823977_S01_A01 7 e6-c3m jc_251197823977_S01_A01.txt e c jc_251197823978_S01_A01 8 c3-e6m jc_251197823978_S01_A01.txt c e jc_251197823989_S01_A01 9 e3-c4m jc_251197823989_S01_A01.txt e c jc_251197823990_S01_A01 10 c4-e3m jc_251197823990_S01_A01.txt c e jc_251197824015_S01_A01 11 e7-c8m jc_251197824015_S01_A01.txt e c jc_251197824017_S01_A01 12 c8-e7m jc_251197824017_S01_A01.txt c e But, if I type 'RG$targets' I get this: e6-c3h jc_16011978013880_S01_A01 c3-e6h jc_16011978013881_S01_A01 e4-c7h jc_16011978013882_S01_A01 c7-e4h jc_251197823977_S01_A01 e7-c8h jc_251197823978_S01_A01 c8-e7h jc_251197823979_S01_A01 e6-c3m jc_251197823980_S01_A01 c3-e6m jc_251197823988_S01_A01 e3-c4m jc_251197823989_S01_A01 c4-e3m jc_251197823990_S01_A01 e7-c8m jc_251197824015_S01_A01 c8-e7m jc_251197824017_S01_A01 So, the slide RG[,2] points to the file 'jc_16011978013881_S01_A01', and has a mismatched name ('c3-e6h')!! If I try (not specifying name=) RG <-read.maimages(source="agilent", ext="txt", path = "C:/Documents and Settings/giovanni/analysis/data",verbose=TRUE, wt.fun=mywtfun(c(1))) ...RG[,2] has no name, but the file ('jc_16011978013881_S01_A01') is still not corresponding to the slide #2 in targets.txt. It looks like read.maimages sorted the files in alphabetical order....without touching the slide names... I can change the file names, but I wonder if I made any mistakes, or this is a point to look at. Thanks Giovanni [[alternative HTML version deleted]]

At 10:02 AM 23/09/2004, Giovanni Coppola wrote: >I am analyzing 12 Agilent slides with LIMMA (ver 1.7.7, R: 1.9.1) >I load my targets file with this line... > >targets<-readTargets(file="targets.txt", path = "C:/Documents and >Settings/giovanni/analysis") > >... and I read the data with this line: > >RG <-read.maimages(name=targets$Name,source="agilent", ext="txt", path = >"C:/Documents and Settings/giovanni/analysis/data",verbose=TRUE, >wt.fun=mywtfun(c(1))) You need RG <- read.maimages(files=targets$FileName, etc If you don't specify 'files', then all the '.ext' files will be read in alphabetical order. If you specify 'names' but not 'files', as you have done, you risk random association of names with files. Gordon >Now, if I type 'targets' I obtain (as expected) the following: > slide.number Name >FileName cy5 cy3 >jc_251197823988_S01_A01 1 >e6-c3h jc_251197823988_S01_A01.txt e c >jc_16011978013880_S01_A01 2 c3-e6h >jc_16011978013880_S01_A01.txt c e >jc_16011978013882_S01_A01 3 e4-c7h >jc_16011978013882_S01_A01.txt e c >jc_16011978013881_S01_A01 4 c7-e4h >jc_16011978013881_S01_A01.txt c e >jc_251197823979_S01_A01 5 >e7-c8h jc_251197823979_S01_A01.txt e c >jc_251197823980_S01_A01 6 >c8-e7h jc_251197823980_S01_A01.txt c e >jc_251197823977_S01_A01 7 >e6-c3m jc_251197823977_S01_A01.txt e c >jc_251197823978_S01_A01 8 >c3-e6m jc_251197823978_S01_A01.txt c e >jc_251197823989_S01_A01 9 >e3-c4m jc_251197823989_S01_A01.txt e c >jc_251197823990_S01_A01 10 >c4-e3m jc_251197823990_S01_A01.txt c e >jc_251197824015_S01_A01 11 >e7-c8m jc_251197824015_S01_A01.txt e c >jc_251197824017_S01_A01 12 >c8-e7m jc_251197824017_S01_A01.txt c e > >But, if I type 'RG$targets' I get this: > >e6-c3h jc_16011978013880_S01_A01 >c3-e6h jc_16011978013881_S01_A01 >e4-c7h jc_16011978013882_S01_A01 >c7-e4h jc_251197823977_S01_A01 >e7-c8h jc_251197823978_S01_A01 >c8-e7h jc_251197823979_S01_A01 >e6-c3m jc_251197823980_S01_A01 >c3-e6m jc_251197823988_S01_A01 >e3-c4m jc_251197823989_S01_A01 >c4-e3m jc_251197823990_S01_A01 >e7-c8m jc_251197824015_S01_A01 >c8-e7m jc_251197824017_S01_A01 > >So, the slide RG[,2] points to the file 'jc_16011978013881_S01_A01', and >has a mismatched name ('c3-e6h')!! > >If I try (not specifying name=) >RG <-read.maimages(source="agilent", ext="txt", path = "C:/Documents and >Settings/giovanni/analysis/data",verbose=TRUE, wt.fun=mywtfun(c(1))) > >...RG[,2] has no name, but the file ('jc_16011978013881_S01_A01') is still >not corresponding to the slide #2 in targets.txt. > >It looks like read.maimages sorted the files in alphabetical >order....without touching the slide names... >I can change the file names, but I wonder if I made any mistakes, or this >is a point to look at. > >Thanks >Giovanni