Hi people,
I execute this step in limma and I have a error below:
> RegianeSample <-
read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> RegianeSample
SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 lamina1BCYE.txt lamina1XDM.txt BCYE XDM
2 2 lamina2BCYE.txt lamina2XDM.txt BCYE XDM
3 3 lamina3BCYE.txt lamina3XDM.txt BCYE XDM
> slides <- RegianeSample$FileName
> RG <- read.maimages(slides, source="imagene")
Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x), :
attempt to set an attribute on NULL
Our out put file is like this (in the original file, lines not is
broken and
names of fields is separated with tab):
Field Meta Row Meta Column Row Column
XDM/BCYE 1 1 1 1
Gene ID Flag Signal Mean Background Mean
Cal 1 1 3.5E+16 8.5E+02
Signal Median Background Median
3.6E+04 8.3E+02
Meta Row range of 1 to 4;
Meta Column range of 1 to 2
Row range of 1 to 32;
Column range of 1 to 24;
Flag is 1, 2 or 3;
Please, any tip are welcome and/or one step by step to analyze imagene
out
put file in limma is very apreciate!
Thanks
Marcelo
---
At 07:34 AM 22/10/2003, Marcelo Luiz de Laia wrote:
>Hi people,
>
>I execute this step in limma and I have a error below:
>
> > RegianeSample <-
>read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> > RegianeSample
> SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
>1 1 lamina1BCYE.txt lamina1XDM.txt BCYE XDM
>2 2 lamina2BCYE.txt lamina2XDM.txt BCYE XDM
>3 3 lamina3BCYE.txt lamina3XDM.txt BCYE XDM
> > slides <- RegianeSample$FileName
> > RG <- read.maimages(slides, source="imagene")
>Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x), :
> attempt to set an attribute on NULL
>
>Our out put file is like this (in the original file, lines not is
broken and
>names of fields is separated with tab):
>
>Field Meta Row Meta Column Row Column
>XDM/BCYE 1 1 1 1
>
>Gene ID Flag Signal Mean Background Mean
>Cal 1 1 3.5E+16 8.5E+02
>
>Signal Median Background Median
>3.6E+04 8.3E+02
>
>Meta Row range of 1 to 4;
>Meta Column range of 1 to 2
>Row range of 1 to 32;
>Column range of 1 to 24;
>Flag is 1, 2 or 3;
>
>Please, any tip are welcome and/or one step by step to analyze
imagene out
>put file in limma is very apreciate!
The above output does not look like an Imagene output file. Where for
example are the "Begin Header", "End Header" and "Begin Raw Data"
lines?
Limma can't be expected to find the data without these sign posts. I
do not
have any direct experience with Imagene, but my guess is that you need
to
go back to Imagene and output the data in the raw data format.
A note to everyone: please specify version numbers for limma and R
when you
ask for help.
Gordon
>Thanks
>
>Marcelo
Updating my previous reply ...
Is is possible that you have edited the Image output files by hand and
removed the header lines? If so, have you also removed the trailing
lines
"End Raw Data" etc at the end of file? If you have, then you can read
the
data in yourself using the R command read.table() and assemble an
RGList
object for yourself. Obviously you have to do this yourself - limma
can't
support user-edited files.
Gordon
At 07:34 AM 22/10/2003, Marcelo Luiz de Laia wrote:
>Hi people,
>
>I execute this step in limma and I have a error below:
>
> > RegianeSample <-
>read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> > RegianeSample
> SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
>1 1 lamina1BCYE.txt lamina1XDM.txt BCYE XDM
>2 2 lamina2BCYE.txt lamina2XDM.txt BCYE XDM
>3 3 lamina3BCYE.txt lamina3XDM.txt BCYE XDM
> > slides <- RegianeSample$FileName
> > RG <- read.maimages(slides, source="imagene")
>Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x), :
> attempt to set an attribute on NULL
>
>Our out put file is like this (in the original file, lines not is
broken and
>names of fields is separated with tab):
>
>Field Meta Row Meta Column Row Column
>XDM/BCYE 1 1 1 1
>
>Gene ID Flag Signal Mean Background Mean
>Cal 1 1 3.5E+16 8.5E+02
>
>Signal Median Background Median
>3.6E+04 8.3E+02
>
>Meta Row range of 1 to 4;
>Meta Column range of 1 to 2
>Row range of 1 to 32;
>Column range of 1 to 24;
>Flag is 1, 2 or 3;
>
>Please, any tip are welcome and/or one step by step to analyze
imagene out
>put file in limma is very apreciate!
>
>Thanks
>
>Marcelo
Hi Gordon,
You are correct! That file was not the real file of the imagene.
However, I
made the same steps with the real file of the imagene and it happens
the
same errors. What can be? I use R 1.8.0 and limma 1.2.8
> library(limma)
> RegianeSample <-
read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> RegianeSample
SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 lamina1_0_selected.txt lamina1_1_selected.txt XDM BCYE
2 2 lamina2_0_selected.txt lamina2_1_selected.txt XDM BCYE
3 3 lamina3_0_selected.txt lamina3_1_selected.txt XDM BCYE
> slides <- RegianeSample$FileName
> RG <- read.maimages(slides, source="imagene")
Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x), :
attempt to set an attribute on NULL
Marcelo
---
Hi Marcelo
Having briefly looked through your script below i think what you need
to do
is change
>slides <- RegianeSample$FileName
to something like
>slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
this should give you a list of the filenames of both the cy3 and cy5
samples. I hope this helps
Pete Underhill
Microarray Facility
MRC Harwell
----- Original Message -----
From: "Marcelo Luiz de Laia" <mlaia@fcav.unesp.br>
To: "Gordon Smyth" <smyth@wehi.edu.au>;
<bioconductor@stat.math.ethz.ch>
Sent: Wednesday, October 22, 2003 4:36 PM
Subject: RE: [BioC] Error with ImaGene out put file in limma
> Hi Gordon,
>
> You are correct! That file was not the real file of the imagene.
However,
I
> made the same steps with the real file of the imagene and it happens
the
> same errors. What can be? I use R 1.8.0 and limma 1.2.8
>
> > library(limma)
> > RegianeSample <-
> read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",as.is=TRUE)
> > RegianeSample
> SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
> 1 1 lamina1_0_selected.txt lamina1_1_selected.txt XDM BCYE
> 2 2 lamina2_0_selected.txt lamina2_1_selected.txt XDM BCYE
> 3 3 lamina3_0_selected.txt lamina3_1_selected.txt XDM BCYE
> > slides <- RegianeSample$FileName
> > RG <- read.maimages(slides, source="imagene")
> Error in array(x, c(length(x), 1), if (!is.null(names(x)))
list(names(x),
:
> attempt to set an attribute on NULL
>
> Marcelo
> ---
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>
Hi Pete,
Thanks very much!!! Your helps was very good!
Now, I have another problem.
I execute the commands above and have this result:
>
RegianeSample<-read.table("regianeRicoPobre.txt",header=TRUE,sep="\t",
as.is=
TRUE)
> RegianeSample
SlideNamber FileNameCy3 FileNameCy5 Cy3 Cy5
1 1 lamina1_0_selected.txt lamina1_1_selected.txt XDM BCYE
2 2 lamina2_0_selected.txt lamina2_1_selected.txt BCYE XDM
3 3 lamina3_0_selected.txt lamina3_1_selected.txt BCYE XDM
> slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
> RG <- read.maimages(slides, source="imagene")
Read header information
Read lamina1_0_selected.txt
Read lamina1_1_selected.txt
Read lamina2_0_selected.txt
Read lamina2_1_selected.txt
Read lamina3_0_selected.txt
Read lamina3_1_selected.txt
> show(RG)
All is correct !!
$printer
$ngrid.r
[1] 4
$ngrid.c
[1] 2
$nspot.r
[1] 32
$nspot.c
[1] 24
$genes
Is OK, too
> MA <- normalizeWithinArrays(RG)
> MA <- normalizeBetweenArrays(MA)
> ?lmFit
> fit <- lmFit(MA, design=c(-1,1,-1,1))
Error in lm.fit(X, y) : incompatible dimensions
> fit <- lmFit(MA, design=c(3,3,3,3))
Error in lm.fit(X, y) : incompatible dimensions
>
Here I have a problem?
I have 3 replicates (3 treated and 3 untread), that correspond to 3
arrays
(slides)!?. But I dont know how much coeficients I will be estimated.
Thanks
Marcelo
-----Original Message-----
From: bioconductor-bounces@stat.math.ethz.ch
[mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Pete
Sent: quarta-feira, 22 de outubro de 2003 13:44
To: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] Error with ImaGene out put file in limma
Hi Marcelo
Having briefly looked through your script below i think what you need
to do
is change
>slides <- RegianeSample$FileName
to something like
>slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
this should give you a list of the filenames of both the cy3 and cy5
samples. I hope this helps
Pete Underhill
Microarray Facility
MRC Harwell
---
---
> Hi Pete,
>
> Thanks very much!!! Your helps was very good!
>
> Now, I have another problem.
>
> I execute the commands above and have this result:
>
>>
> RegianeSample<-read.table("regianeRicoPobre.txt",header=TRUE,sep="\t
",as.is=
> TRUE)
>> RegianeSample
> SlideNamber FileNameCy3 FileNameCy5 Cy3
Cy5
> 1 1 lamina1_0_selected.txt lamina1_1_selected.txt XDM
BCYE 2
> 2 lamina2_0_selected.txt lamina2_1_selected.txt BCYE XDM 3
> 3 lamina3_0_selected.txt lamina3_1_selected.txt BCYE XDM
>> slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
RG
>> <- read.maimages(slides, source="imagene")
> Read header information
> Read lamina1_0_selected.txt
> Read lamina1_1_selected.txt
> Read lamina2_0_selected.txt
> Read lamina2_1_selected.txt
> Read lamina3_0_selected.txt
> Read lamina3_1_selected.txt
>> show(RG)
> All is correct !!
> $printer
> $ngrid.r
> [1] 4
> $ngrid.c
> [1] 2
> $nspot.r
> [1] 32
> $nspot.c
> [1] 24
> $genes
> Is OK, too
>> MA <- normalizeWithinArrays(RG)
>> MA <- normalizeBetweenArrays(MA)
>> ?lmFit
>> fit <- lmFit(MA, design=c(-1,1,-1,1))
You have 3 arrays but you've given 4 numbers. You need just
design=c(-1,1,-1).
> Error in lm.fit(X, y) : incompatible dimensions
>> fit <- lmFit(MA, design=c(3,3,3,3))
> Error in lm.fit(X, y) : incompatible dimensions
>>
>
> Here I have a problem?
>
> I have 3 replicates (3 treated and 3 untread), that correspond to 3
> arrays (slides)!?. But I dont know how much coeficients I will be
> estimated.
You only have one comparison to make: BCYE vs XDM, so there is only
coefficient, regardless of number of arrays.
Gordon
>
> Thanks
>
> Marcelo
> -----Original Message-----
> From: bioconductor-bounces@stat.math.ethz.ch
> [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of Pete
> Sent: quarta-feira, 22 de outubro de 2003 13:44
> To: bioconductor@stat.math.ethz.ch
> Subject: Re: [BioC] Error with ImaGene out put file in limma
>
>
> Hi Marcelo
> Having briefly looked through your script below i think what you
need to
> do is change
>
>
>>slides <- RegianeSample$FileName
>
> to something like
>
>>slides<-cbind(RegianeSample$FileNameCy3, RegianeSample$FileNameCy5)
>
> this should give you a list of the filenames of both the cy3 and cy5
> samples. I hope this helps
>
>
> Pete Underhill
>
> Microarray Facility
> MRC Harwell
> ---
>
>
>
> ---
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
Hi Gordon and All.
I suspect that my doubts are very basic! I am sorry for this! However,
the
maillist is the only way that I have to solve these doubts. I can say
that
am being very well helped.
But, I have another doubt, and, possibly, have others:
When I typed the command below,
>fit <- lmFit(MA, design=c(-1,1,-1))
>fit <- eBayes(fit)
>options(digits=3)
>topTable(fit, n=30, adjust="fdr")
>plot.print.tip.lowess(RG,layout,pch=16,cex=0.1,image=3)
it opened up a new window and appeared the graph of dispersion of
points,
without the tendency line and the following error:
Error in 1:npin : NA/NaN argument
When I typed this other command, appeared only the error:
Error in 1:npin : NA/NaN argument
What can be?
Marcelo
---
