Hi Jo?o,
As Hans-Ulrich said, the default value of plotMA is to not plot spots
with
weight = 0. However, if you want to keep your flags set at weight=0.1,
but
not plot them, you just weren't subsetting the RG$weights correctly;
to
plot array 1, you have to subset the RG$weights for array/column 1:
plotMA(RG[(RG$weights[,1])>0.1,], array=1)
Cheers,
Jenny
At 01:22 AM 12/21/2006, Jo?o Fadista wrote:
>Content-Disposition: inline
>Content-Type: text/plain
>Content-length: 1378
>
>Dear all,
>
>I am not able to plot only the MA values for the spots with no flags.
Here
>is my code and the error:
>
>RG <- read.maimages(fnames, source="genepix", path=datadir,
ext="gpr",
>columns=columns, wt.fun=wtflags(0.1))
>RG$printer <- getLayout(RG$genes,guessdups=TRUE)
>types <- readSpotTypes("SpotTypes.txt",path=genedir)
>RG$genes$Status <- controlStatus(types, RG)
>
> > plotMA(RG[(RG$weights)>0.1,], array=1)
>Error in `[.RGList`(RG, (RG$weights) > 0.1, ) :
> (subscript) logical subscript too long
>
>
>Does anybody know how to do it?
>
>
>
>Best regards
>
>Jo?o Fadista
>Ph.d. student
>
>
>
> Danish Institute of Agricultural Sciences
>Research Centre Foulum
>Dept. of Genetics and Biotechnology
>Blichers All? 20, P.O. BOX 50
>DK-8830 Tjele
>
>Phone: +45 8999 1900
>Direct: +45 8999 8999
>E-mail: Joao.Fadista at agrsci.dk <mailto:joao.fadista at="" agrsci.dk="">
>Web: www.agrsci.org <http: www.agrsci.org=""/>
>________________________________
>
>News and news media
<http: www.agrsci.org="" navigation="" nyheder_og_presse=""> .
>
>This email may contain information that is confidential. Any use or
>publication of this email without written permission from DIAS is not
>allowed. If you are not the intended recipient, please notify DIAS
>immediately and delete this email.
>
>
> [[alternative HTML version deleted]]
>
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
>Search the archives:
>http://news.gmane.org/gmane.science.biology.informatics.conductor
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign
330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA
ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu
Jo?o Fadista wrote:
>[...]
>
>
>>plotMA(RG[(RG$weights)>0.1,], array=1)
>>
>>
>Error in `[.RGList`(RG, (RG$weights) > 0.1, ) :
> (subscript) logical subscript too long
>
>
Dear Joao,
you can try
> RG$weights <- RG$weights - 0.1;
> plotMA(RG, array=1, zero.weights=FALSE);
> RG$weights <- RG$weights + 0.1;
If the argument zero.weights is set to FALSE (default value), plotMA()
omits spots with a weight less or equal 0.
Regards,
Hans-Ulrich
--
Westf?lische Wilhelms-Universit?t M?nster
Department of Medical Informatics and Biomathematics
Hans-Ulrich Klein, Domagkstr. 9, Raum 27, 48149 M?nster
