Dear Marcus and group,
Thanks for the information!
However, for some odd reason, when I try to run makeContrasts() in a  
function, it cannot recognize the expression or a character string,  
in this case "difference"...
It works well when I run it directly on a console, but not as a  
function. Do you know why this could happen?
thank you.

Jay

On Aug 3, 2006, at 1:37 AM, Marcus Davy wrote:

>
> Hi,
> member[2] - member[3] is going to give an error os the binary  
> operator "-"
> cannot operate on strings,
>
>> member[2] - member[3]
> Error in member[2] - member[3] : non-numeric argument to binary  
> operator
>
> try,
>
> design <- diag(3)[rep(1:3, each=2),]
> colnames(design) <- member
> member <- LETTERS[1:3]
>
> difference <- paste(member[2],"-",member[3], sep="")
> makeContrasts(difference,levels=design)
>
>
> Marcus
>
>
> On 8/2/06 7:00 PM, "Jay Shin" <jay.shin@pharma.ethz.ch> wrote:
>
>> Hello,
>> I am trying to run a makeConstrasts() function to compute eBayes t-
>> test with the following design list (six hybridizations and three
>> samples -in duplicates):
>> A   B    C
>> 1    1   0    0
>> 2    1   0    0
>> 3    0   1    0
>> 4    0   1    0
>> 5    0   0    1
>> 6    0   0    1
>>
>> I would like to compare sample "B-C", so when I run:
>>> contrasts.matrix<-makeContrasts(B-C, levels=design)
>> it works great!
>>
>> However, I have B and C stored in 'member' (e.g. member[1] = B,  
>> member
>> [2] = C).
>> So, when I try to run:
>>> member1<-member[1]
>>> member2<-member[2]
>>> contrasts.matrix<-makeContrasts(member1-member2, levels=design)
>>
>>   I get a following error message:
>> Error in eval(expr, envir, enclos) : object "member1" not found
>>
>> Can you please help me how I can directly compare the content of the
>> 'member' in makeContrasts() function?
>> Thank you,
>> Jay
>>
>> On Aug 2, 2006, at 4:40 AM, Gordon Smyth wrote:
>>
>>> Dear Bjoern,
>>>
>>>> Date: Mon, 31 Jul 2006 12:43:00 +0200
>>>> From: Bj?rn Usadel <usadel@mpimp-golm.mpg.de>
>>>> Subject: [BioC] limma: read.maimages possibility to warn the user?
>>>> To: bioconductor@stat.math.ethz.ch
>>>>
>>>> Dear list,
>>>>
>>>> when using read.maimages from limma with a "broken" file (tabs
>>>> replaced
>>>> by ":", two extra tabs added at the end of row e)
>>>> limma reads the table fine
>>>>
>>>> table:
>>>> :R:G:RB:GB
>>>> a:1:2:0.5:0.5
>>>> b:2:4:1:1
>>>> c:3:6:1.5:1.5
>>>> d:4:8:2:2
>>>> e:5:10:2.5:2.5::
>>>> f:6:12:3:3
>>>> g:7:14:3.5:3.5
>>>>
>>>> code:
>>>> RG<-read.maimages(files="test.txt", path="C://cpan//",columns=list
>>>> (Gf="G",
>>>>                                             Rf="R",
>>>>                                             Gb="GB",
>>>>                                             Rb="RB"
>>>>                                             ))
>>>>
>>>> But I get NA values added in all columns thus changing the order of
>>>> probes in this particular arrayfile
>>>> $G
>>>>       test
>>>> [1,]    2
>>>> [2,]    4
>>>> [3,]    6
>>>> [4,]    8
>>>> [5,]   10
>>>> [6,]   NA  <-
>>>> [7,]   12
>>>> [8,]   14
>>>
>>> This unfortunate behaviour is due to (what I believe to be) a bug in
>>> the R function read.table. (I've sent a post to R-devel today to
>>> discuss it.) You can prevent it simply by adding the argument
>>> flush=TRUE to your read.maimages() call. This will result in the
>>> spurious delimiters at the of the end of the lines being ignored.
>>>
>>> Perhaps I will add flush=TRUE to the limma read by default.
>>>
>>>> Marray on the other hand, complains using the following syntax and
>>>> refuses to read in the offending file.
>>>> RG2<-read.marrayRaw(fnames="test.txt",path="C://cpan//",  
>>>> name.Gf="G",
>>>>                                             name.Rf="R",
>>>>                                             name.Gb="GB",
>>>>                                             name.Rb="RB"
>>>>                                             )
>>>>
>>>> "Error in scan(file = file, what = what, sep = sep, quote = quote,
>>>> dec =
>>>> dec,  :   line 5 did not have 5 elements"
>>>
>>> This is something of an accident. If there had been five extra tab
>>> characters at the end of the line instead of two, then marray would
>>> have done exactly the same as limma. The difference between the two
>>> packages is that limma is using fill=TRUE in the read while  
>>> marray is
>>> not. This allows limma to read incomplete lines.
>>>
>>> Best wishes
>>> Gordon
>>>
>>>> Even though I appreciate, that limma reads the data fine without  
>>>> the
>>>> usual read.table hazzle and realize that the data should have been
>>>> checked before reading it in anyway, I think at least a little
>>>> warning
>>>> could greatly help.
>>>> But maybe I missed something important (not being a two color type
>>>> anyway)?
>>>>
>>>> (The broken files result from an MS Excel export and this  
>>>> happens on
>>>> R2.2 with limma 2.4.13 and on R 2.3.1 with limma 2.6.2)
>>>>
>>>>
>>>> Cheers,
>>>> Bj?rn
>>>>
>>>>
>>>> --
>>>> -+-+-+-+-+-+-+-+-+-+-+-
>>>> Bj?rn Usadel, PhD
>>>>
>>>> Max Planck Institute of Molecular Plant Physiology
>>>> System Regulation Group
>>>>
>>>> Am M?hlenberg 1
>>>> D-14476 Golm
>>>> Germany
>>>>
>>>> Tel    (+49 331) 567-8114
>>>>
>>>> Email  usadel@mpimp-golm.mpg.de
>>>> WWW    mapman.mpimp-golm.mpg.de
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/
>>> gmane.science.biology.informatics.conductor
>>
>> ________________________________________________________
>> ETH Zurich
>> Jay W. Shin
>> Institute of Pharmaceutical Sciences
>> HCI H394
>> Wolfgang-Paulistrasse 10
>> 8093 Zurich, Switzerland
>>
>> jay.shin@pharma.ethz.ch
>> www.pharma.ethz.ch
>>
>> ++41 44 633 73 68 phone
>> ++41 44 633 13 64 fax
>>
>>
>>
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>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
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________________________________________________________
ETH Zurich
Jay W. Shin
Institute of Pharmaceutical Sciences
HCI H394
Wolfgang-Paulistrasse 10
8093 Zurich, Switzerland

jay.shin@pharma.ethz.ch
www.pharma.ethz.ch

++41 44 633 73 68 phone
++41 44 633 13 64 fax



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