Dear Joao,
See ?plotPrintorder and
http://www.statsci.org/smyth/pubs/porder/porder.html. (I'm a bit
puzzled why you haven't already tried this, considering that you're
already using limma and are aware of printorder effects.)
Note that GAL file order is not the same as printorder in general, so
you can't just use plot().
Best wishes
Gordon
>Date: Fri, 22 Dec 2006 19:33:11 +0000
>From: J.delasHeras at ed.ac.uk
>Subject: Re: [BioC] Plate or print-order effects - limma
>To: bioconductor at stat.math.ethz.ch
>
>Just use 'plot':
>
>is MA is teh name of your MAlist containing your M and A values, then
>
>plot(MA$A[,1],MA$M[,1]) #prints the usual MA plot for slide 1
>
>plot(MA$M[,1]) #prints the M values, in the order given in the gal
>file (by block)... is that what you wanted?
>
>just add your favourite parameters to 'plot' to make it look the way
>you want it.
>
>Jose
>
>
>Quoting Jo?o Fadista <joao.fadista at="" agrsci.dk="">:
>
> > Dear all,
> >
> > I would like to visualize, for each array, the plate or print-
order
> > effects. To do that I want to be able to plot the M values in the
> > vertical axis and the print order (i.e., the numerical order in
> > which the spots were laid down during the printing of the array)
in
> > the horizontal axis. I am using genepix files.
> >
> > Thanks in advance,
> >
> > 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]]
> >
> >
>
>
>
>--
>Dr. Jose I. de las Heras Email: J.delasHeras at
ed.ac.uk
>The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
6513374
>Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
>Swann Building, Mayfield Road
>University of Edinburgh
>Edinburgh EH9 3JR
>UK
Hi Gordon,
FYI - I was playing around with plotting print order effects, and
found a
discrepancy between the help documentation and the actual behavior of
'normalizeForPrintorder.rg '. The help file states "The function
plotPrintorder or normalizeForPrintorder.rg with plot=TRUE returns no
value
but produces a plot as a side-effect." However, when I used
'normalizeForPrintorder.rg' with plot=TRUE, it not only produced the
plot
but spit out the entire list!
I'm using this function instead of the wrapper 'plotPrintorder'
because I'm
having trouble making the necessary layout list. I could only find a
little
bit of information about the layout list in 'printorder' help page -
is
each component of the list (ngrid.r, ngrid.c, nspot.r and nspot.c)
just a
single number? In my case our printer has 48 tips and prints 12 x 4
blocks
of 420 spots, one dip per spot, so would my layout just be a list of
ngrid.r = 12, ngrid.c = 4, nspot.r = 420, and nspot.c = 1?
Thanks,
Jenny
> sessionInfo()
R version 2.4.0 (2006-10-03)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
[7] "utils" "datasets" "base"
other attached packages:
affyQCReport simpleaffy made4 scatterplot3d ade4
"1.12.0" "2.8.0" "1.8.0" "0.3-24" "1.4-2"
affyPLM affydata affycoretools annaffy xtable
"1.10.0" "1.10.0" "1.7.5" "1.6.0" "1.4-2"
gcrma matchprobes biomaRt RCurl XML
"2.6.0" "1.6.0" "1.8.0" "0.7-0" "1.2-0"
GOstats Category genefilter survival KEGG
"2.0.3" "2.0.3" "1.12.0" "2.29" "1.14.1"
RBGL annotate GO graph limma
"1.10.0" "1.12.0" "1.14.1" "1.12.0" "2.9.1"
affy affyio Biobase RWinEdt
"1.12.1" "1.2.0" "1.12.2" "1.7-5"
At 09:32 PM 12/31/2006, Gordon Smyth wrote:
>Dear Joao,
>
>See ?plotPrintorder and
>http://www.statsci.org/smyth/pubs/porder/porder.html. (I'm a bit
>puzzled why you haven't already tried this, considering that you're
>already using limma and are aware of printorder effects.)
>
>Note that GAL file order is not the same as printorder in general, so
>you can't just use plot().
>
>Best wishes
>Gordon
>
> >Date: Fri, 22 Dec 2006 19:33:11 +0000
> >From: J.delasHeras at ed.ac.uk
> >Subject: Re: [BioC] Plate or print-order effects - limma
> >To: bioconductor at stat.math.ethz.ch
> >
> >Just use 'plot':
> >
> >is MA is teh name of your MAlist containing your M and A values,
then
> >
> >plot(MA$A[,1],MA$M[,1]) #prints the usual MA plot for slide 1
> >
> >plot(MA$M[,1]) #prints the M values, in the order given in the gal
> >file (by block)... is that what you wanted?
> >
> >just add your favourite parameters to 'plot' to make it look the
way
> >you want it.
> >
> >Jose
> >
> >
> >Quoting Jo?o Fadista <joao.fadista at="" agrsci.dk="">:
> >
> > > Dear all,
> > >
> > > I would like to visualize, for each array, the plate or print-
order
> > > effects. To do that I want to be able to plot the M values in
the
> > > vertical axis and the print order (i.e., the numerical order in
> > > which the spots were laid down during the printing of the array)
in
> > > the horizontal axis. I am using genepix files.
> > >
> > > Thanks in advance,
> > >
> > > 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]]
> > >
> > >
> >
> >
> >
> >--
> >Dr. Jose I. de las Heras Email: J.delasHeras
at ed.ac.uk
> >The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
6513374
> >Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
> >Swann Building, Mayfield Road
> >University of Edinburgh
> >Edinburgh EH9 3JR
> >UK
>
>_______________________________________________
>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
Dear Jenny
As I recall, ngrid.r & ngrid.c are the number of grid rows and
columns, so
12 and 4 in your case, while nspot.r & nspot.c are the number of spot
rows
and columns within each grid block, probably 20 and 21 for you. I
don't
think the number of dips per spot is taken into account.
HTH
\Heidi
> ...I could only find a little
> bit of information about the layout list in 'printorder' help page -
is
each component of the list (ngrid.r, ngrid.c, nspot.r and nspot.c)
just
a
> single number? In my case our printer has 48 tips and prints 12 x 4
blocks
> of 420 spots, one dip per spot, so would my layout just be a list of
ngrid.r = 12, ngrid.c = 4, nspot.r = 420, and nspot.c = 1?
>
> Thanks,
> Jenny
>
> > sessionInfo()
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] "splines" "tools" "methods" "stats" "graphics"
> "grDevices"
> [7] "utils" "datasets" "base"
>
> other attached packages:
> affyQCReport simpleaffy made4 scatterplot3d
ade4
> "1.12.0" "2.8.0" "1.8.0" "0.3-24"
"1.4-2"
> affyPLM affydata affycoretools annaffy
xtable
> "1.10.0" "1.10.0" "1.7.5" "1.6.0"
"1.4-2"
> gcrma matchprobes biomaRt RCurl
XML
> "2.6.0" "1.6.0" "1.8.0" "0.7-0"
"1.2-0"
GOstats Category genefilter survival KEGG
"2.0.3" "2.0.3" "1.12.0" "2.29" "1.14.1"
> RBGL annotate GO graph
limma
> "1.10.0" "1.12.0" "1.14.1" "1.12.0"
"2.9.1"
> affy affyio Biobase RWinEdt
> "1.12.1" "1.2.0" "1.12.2" "1.7-5"
>
>
> At 09:32 PM 12/31/2006, Gordon Smyth wrote:
>>Dear Joao,
>>See ?plotPrintorder and
>>http://www.statsci.org/smyth/pubs/porder/porder.html. (I'm a bit
puzzled
why you haven't already tried this, considering that you're already
using limma and are aware of printorder effects.)
>>Note that GAL file order is not the same as printorder in general,
so
you can't just use plot().
>>Best wishes
>>Gordon
>> >Date: Fri, 22 Dec 2006 19:33:11 +0000
>> >From: J.delasHeras at ed.ac.uk
>> >Subject: Re: [BioC] Plate or print-order effects - limma
>> >To: bioconductor at stat.math.ethz.ch
>> >
>> >Just use 'plot':
>> >
>> >is MA is teh name of your MAlist containing your M and A values,
then
>> >
>> >plot(MA$A[,1],MA$M[,1]) #prints the usual MA plot for slide 1
>> >
>> >plot(MA$M[,1]) #prints the M values, in the order given in the gal
file (by block)... is that what you wanted?
>> >
>> >just add your favourite parameters to 'plot' to make it look the
way
you want it.
>> >
>> >Jose
>> >
>> >
>> >Quoting Jo?o Fadista <joao.fadista at="" agrsci.dk="">:
>> >
>> > > Dear all,
>> > >
>> > > I would like to visualize, for each array, the plate or print-
order
effects. To do that I want to be able to plot the M values in the
vertical axis and the print order (i.e., the numerical order in
which the spots were laid down during the printing of the array) in
the horizontal axis. I am using genepix files.
>> > >
>> > > Thanks in advance,
>> > >
>> > > 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]]
>> > >
>> > >
>> >
>> >
>> >
>> >--
>> >Dr. Jose I. de las Heras Email:
>> J.delasHeras at ed.ac.uk
>> >The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
6513374
>> >Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
>> >Swann Building, Mayfield Road
>> >University of Edinburgh
>> >Edinburgh EH9 3JR
>> >UK
>>_______________________________________________
>>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
>
> _______________________________________________
> 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
>
At 07:38 AM 3/01/2007, Jenny Drnevich wrote:
>Hi Gordon,
>
>FYI - I was playing around with plotting print order effects, and
>found a discrepancy between the help documentation and the actual
>behavior of 'normalizeForPrintorder.rg '. The help file states "The
>function plotPrintorder or normalizeForPrintorder.rg with plot=TRUE
>returns no value but produces a plot as a side-effect." However,
>when I used 'normalizeForPrintorder.rg' with plot=TRUE, it not only
>produced the plot but spit out the entire list!
You're right. I'll fix.
>I'm using this function instead of the wrapper 'plotPrintorder'
>because I'm having trouble making the necessary layout list. I could
>only find a little bit of information about the layout list in
>'printorder' help page - is each component of the list (ngrid.r,
>ngrid.c, nspot.r and nspot.c) just a single number? In my case our
>printer has 48 tips and prints 12 x 4 blocks of 420 spots, one dip
>per spot, so would my layout just be a list of ngrid.r = 12, ngrid.c
>= 4, nspot.r = 420, and nspot.c = 1?
You also need to know the number of rows (nspot.r) and columns
(nspot.c) of spots in each block. nspot.c is almost certainly greater
than 1.
You also need to check with your microarray printing unit whether
printing of your arrays begins in the top right or top left of each
block, and whether it proceeds by rows or columns. The default for
normalizeForPrintorder assumes topleft by rows, which the usual setup
at UCSF. But the AGRF in Australia uses topright by rows.
See help("PrinterLayout-class"). The read.maimages() function
produces the printer layout information automatically as RG$printer
for some input sources including GenePix and ImageGene.
Best wishes
Gordon
>Thanks,
>Jenny
>
> > sessionInfo()
>R version 2.4.0 (2006-10-03)
>i386-pc-mingw32
>
>locale:
>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>States.1252;LC_MONETARY=English_United
>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>attached base packages:
>[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
>[7] "utils" "datasets" "base"
>
>other attached packages:
> affyQCReport simpleaffy made4 scatterplot3d
ade4
> "1.12.0" "2.8.0" "1.8.0" "0.3-24"
"1.4-2"
> affyPLM affydata affycoretools annaffy
xtable
> "1.10.0" "1.10.0" "1.7.5" "1.6.0"
"1.4-2"
> gcrma matchprobes biomaRt RCurl
XML
> "2.6.0" "1.6.0" "1.8.0" "0.7-0"
"1.2-0"
> GOstats Category genefilter survival
KEGG
> "2.0.3" "2.0.3" "1.12.0" "2.29"
"1.14.1"
> RBGL annotate GO graph
limma
> "1.10.0" "1.12.0" "1.14.1" "1.12.0"
"2.9.1"
> affy affyio Biobase RWinEdt
> "1.12.1" "1.2.0" "1.12.2" "1.7-5"
>
>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
Hi Gordon,
Thanks for your help. Here's one correction for the archives and a
small
suggestion:
>See help("PrinterLayout-class").
this should be help("PrintLayout-class")
>The read.maimages() function produces the printer layout information
>automatically as RG$printer for some input sources including GenePix
and
>ImageGene.
The PrintLayout class help page does explain everything pretty well,
and I
was happy to see that I already had RG$printer because I had GenePix
data.
I would suggest a small change to the help page of Print-Order
Normalization, that the argument 'layout' wants an object of class
'PrintLayout' (or a similar list). That would have helped me make the
connection and find the information.
Thanks,
Jenny
>Best wishes
>Gordon
>
>>Thanks,
>>Jenny
>>
>> > sessionInfo()
>>R version 2.4.0 (2006-10-03)
>>i386-pc-mingw32
>>
>>locale:
>>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>>States.1252;LC_MONETARY=English_United
>>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>>attached base packages:
>>[1] "splines" "tools" "methods" "stats" "graphics"
"grDevices"
>>[7] "utils" "datasets" "base"
>>
>>other attached packages:
>> affyQCReport simpleaffy made4 scatterplot3d
ade4
>> "1.12.0" "2.8.0" "1.8.0" "0.3-24"
"1.4-2"
>> affyPLM affydata affycoretools annaffy
xtable
>> "1.10.0" "1.10.0" "1.7.5" "1.6.0"
"1.4-2"
>> gcrma matchprobes biomaRt RCurl
XML
>> "2.6.0" "1.6.0" "1.8.0" "0.7-0"
"1.2-0"
>> GOstats Category genefilter survival
KEGG
>> "2.0.3" "2.0.3" "1.12.0" "2.29"
"1.14.1"
>> RBGL annotate GO graph
limma
>> "1.10.0" "1.12.0" "1.14.1" "1.12.0"
"2.9.1"
>> affy affyio Biobase RWinEdt
>> "1.12.1" "1.2.0" "1.12.2" "1.7-5"
>>
>>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
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
On Thu, January 4, 2007 3:43 am, Jenny Drnevich wrote:
> Hi Gordon,
>
> Thanks for your help. Here's one correction for the archives and a
small
> suggestion:
>
>>See help("PrinterLayout-class").
>
> this should be help("PrintLayout-class")
>
>
>>The read.maimages() function produces the printer layout information
>>automatically as RG$printer for some input sources including GenePix
and
>>ImageGene.
>
> The PrintLayout class help page does explain everything pretty well,
and I
> was happy to see that I already had RG$printer because I had GenePix
data.
> I would suggest a small change to the help page of Print-Order
> Normalization, that the argument 'layout' wants an object of class
> 'PrintLayout' (or a similar list). That would have helped me make
the
> connection and find the information.
Fixed.
Best wishes
Gordon
> Thanks,
> Jenny
Dear Gordon Smyth,
Thanks for the information. Concerning the analysis of variance that
you did in http://www.statsci.org/smyth/pubs/porder/porder.html, I
would like to know how did you made the table in that format, with
between and within genes?
Kind regards,
Jo?o Fadista
-----Original Message-----
From: Gordon Smyth [mailto:smyth@wehi.EDU.AU]
Sent: Monday, January 01, 2007 4:32 AM
To: J.delasHeras at ed.ac.uk; Jo?o Fadista
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] Plate or print-order effects - limma
Dear Joao,
See ?plotPrintorder and
http://www.statsci.org/smyth/pubs/porder/porder.html. (I'm a bit
puzzled why you haven't already tried this, considering that you're
already using limma and are aware of printorder effects.)
Note that GAL file order is not the same as printorder in general, so
you can't just use plot().
Best wishes
Gordon
>Date: Fri, 22 Dec 2006 19:33:11 +0000
>From: J.delasHeras at ed.ac.uk
>Subject: Re: [BioC] Plate or print-order effects - limma
>To: bioconductor at stat.math.ethz.ch
>
>Just use 'plot':
>
>is MA is teh name of your MAlist containing your M and A values, then
>
>plot(MA$A[,1],MA$M[,1]) #prints the usual MA plot for slide 1
>
>plot(MA$M[,1]) #prints the M values, in the order given in the gal
file
>(by block)... is that what you wanted?
>
>just add your favourite parameters to 'plot' to make it look the way
>you want it.
>
>Jose
>
>
>Quoting Jo?o Fadista <joao.fadista at="" agrsci.dk="">:
>
> > Dear all,
> >
> > I would like to visualize, for each array, the plate or print-
order
> > effects. To do that I want to be able to plot the M values in the
> > vertical axis and the print order (i.e., the numerical order in
> > which the spots were laid down during the printing of the array)
in
> > the horizontal axis. I am using genepix files.
> >
> > Thanks in advance,
> >
> > Best regards
> >
> > Jo?o Fadista
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>Dr. Jose I. de las Heras Email: J.delasHeras at
ed.ac.uk
>The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
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Dear Joao,
I don't remember how I made the anova table. The information can be
obtained from two one-way
anovas and I probably made the table by hand.
Best wishes
Gordon
On Wed, January 3, 2007 11:00 pm, Jo?o Fadista wrote:
> Dear Gordon Smyth,
>
> Thanks for the information. Concerning the analysis of variance that
you did in
> http://www.statsci.org/smyth/pubs/porder/porder.html, I would like
to know how did you made the
> table in that format, with between and within genes?
>
> Kind regards,
> Jo?o Fadista