[BioC] limma: makeContrasts()
Marcus Davy
mdavy at hortresearch.co.nz
Thu Aug 3 01:37:41 CEST 2006
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 at 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 at mpimp-golm.mpg.de>
>>> Subject: [BioC] limma: read.maimages possibility to warn the user?
>>> To: bioconductor at 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 at mpimp-golm.mpg.de
>>> WWW mapman.mpimp-golm.mpg.de
>>
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
> ________________________________________________________
> ETH Zurich
> Jay W. Shin
> Institute of Pharmaceutical Sciences
> HCI H394
> Wolfgang-Paulistrasse 10
> 8093 Zurich, Switzerland
>
> jay.shin at pharma.ethz.ch
> www.pharma.ethz.ch
>
> ++41 44 633 73 68 phone
> ++41 44 633 13 64 fax
>
>
>
> [[alternative HTML version deleted]]
>
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