[BioC] limma & targets

Giovanni Coppola gcoppola at ucla.edu
Thu Sep 23 02:02:53 CEST 2004

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 

... 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, 

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.


	[[alternative HTML version deleted]]

More information about the Bioconductor mailing list