[BioC] Error with lmFit
Sara Rollinson
Sara.Rollinson at egu.york.ac.uk
Tue Apr 26 13:12:40 CEST 2005
Dear Anyone- can you help me
I'm trying to use limma to do a time course analysis using affymetrix
data, I'm new to R so I guess I'm doing something really silly so I'm
sorry if I'm being stupid. I've tried searching the archive and I'm no
wiser.
Also sorry about the length of this posting, I wanted to try and cover
everything I've tried.
I've installed R version 2.0.1 and used the Packages option to install
the Affy and Limma packages, can I just say that's really easy!, very
nice pdf file help to :-)
I started by using the affy package to read in my cel files from the
directory I set
Data<- ReadAffy()
And for speeds sake am first trying the rma option to normalize
Eset <-rma(Data)
Which gives me
> eset
Expression Set (exprSet) with
22810 genes
24 samples
phenoData object with 1 variables and 26 cases
varLabels
sample: arbitrary numbering
I've also loaded a Targets file as below
FileName
Target
30MIN_SHOOT_REP1 30MIN_SHOOT_REP1.CEL con0.5hr
30MIN_SHOOT_REP2 30MIN_SHOOT_REP2.CEL con0.5hr
Etc with different times and a treatment set, a set of replicates per
sample.
Obviously, I was being a bit ambitious, I used the info given on page 35
of the limma manual to try and analyze my time course data as per the
example
> lev<- c("con0.5hr", "con1hr","con3hr", "con6hr", "con12hr", "con24hr",
+ "tre0.5hr", "tre1hr", "tre3hr", "tre6hr", "tre12hr", "tre24hr")
which gives me
> lev
[1] "con0.5hr" "con1hr" "con3hr" "con6hr" "con12hr" "con24hr"
[7] "tre0.5hr" "tre1hr" "tre3hr" "tre6hr" "tre12hr" "tre24hr"
then
> f <- factor(targets$Target, levels=lev)
> f
[1] con0.5hr con0.5hr con1hr con1hr con3hr con3hr con6hr
con6hr
[9] con12hr con12hr con24hr con24hr tre0.5hr tre0.5hr tre1hr
tre1hr
[17] tre3hr tre3hr tre6hr tre6hr tre12hr tre12hr tre24hr
tre24hr
12 Levels: con0.5hr con1hr con3hr con6hr con12hr con24hr tre0.5hr ...
tre24hr
then design the model matrix
design <- model.matrix(~0+f)
> design
fcon0.5hr fcon1hr fcon3hr fcon6hr fcon12hr fcon24hr ftre0.5hr ftre1hr
1 1 0 0 0 0 0 0 0
2 1 0 0 0 0 0 0 0
3 0 1 0 0 0 0 0 0
4 0 1 0 0 0 0 0 0
5 0 0 1 0 0 0 0 0
6 0 0 1 0 0 0 0 0
7 0 0 0 1 0 0 0 0
8 0 0 0 1 0 0 0 0
9 0 0 0 0 1 0 0 0
10 0 0 0 0 1 0 0 0
11 0 0 0 0 0 1 0 0
12 0 0 0 0 0 1 0 0
13 0 0 0 0 0 0 1 0
14 0 0 0 0 0 0 1 0
15 0 0 0 0 0 0 0 1
16 0 0 0 0 0 0 0 1
17 0 0 0 0 0 0 0 0
18 0 0 0 0 0 0 0 0
19 0 0 0 0 0 0 0 0
20 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0
24 0 0 0 0 0 0 0 0
ftre3hr ftre6hr ftre12hr ftre24hr
1 0 0 0 0
2 0 0 0 0
3 0 0 0 0
4 0 0 0 0
5 0 0 0 0
6 0 0 0 0
7 0 0 0 0
8 0 0 0 0
9 0 0 0 0
10 0 0 0 0
11 0 0 0 0
12 0 0 0 0
13 0 0 0 0
14 0 0 0 0
15 0 0 0 0
16 0 0 0 0
17 1 0 0 0
18 1 0 0 0
19 0 1 0 0
20 0 1 0 0
21 0 0 1 0
22 0 0 1 0
23 0 0 0 1
24 0 0 0 1
attr(,"assign")
[1] 1 1 1 1 1 1 1 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$f
[1] "contr.treatment"
Then
> colnames(design)<-lev
> colnames(design)
[1] "con0.5hr" "con1hr" "con3hr" "con6hr" "con12hr" "con24hr"
[7] "tre0.5hr" "tre1hr" "tre3hr" "tre6hr" "tre12hr" "tre24hr"
But when I do lmFit I get
> fit <-lmFit(eset,design)
Error in lm.fit(design, t(M)) : incompatible dimensions
So I tested if my expression set is a data.frame as I think it is
supposed to be
> is.data.frame(eset)
[1] FALSE
So then I tried importing my pre-normalized values into a data table
using
data<-read.csv("mydata.csv", header = TRUE, sep = ',')
> is.data.frame(data)
[1] TRUE
and is formatted as following (the header names being as the targets
file, shortened here to fit on screen)
X 30MINREP1 30MINREP2
1 244901_at 6.34848 6.128339
etc for miles!
But I get the same lmfit error as before?
<-lmFit(data,design)
Error in lm.fit(design, t(M)) : incompatible dimensions
Can anyone give me any help, I guess I'm missing something basic, I
think I have a different problem with the eset and the imported data
file but am really stuck.
Many thanks in advance for any help anyone can give me
Sara Rollinson
Dr Sara Rollinson,
Academic Unit of Oncology and Haematology,
Algernon Firth Building,
Great George Street,
University of Leeds,
Leeds,
Ls2 9JT.
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