Arne.Muller | 1 Dec 11:25 2004

RE: normalisation or analysis with batch effects

Hello,

the 11 tumour sampel are considered as biological replicates, or are these split into different tumour classes?

We've had a similar problem. Our data was generated in three different laboratories, each having slightly
different protocols, but within each lab we had the same factors (the same doses of a drug).

I guess, if the tumours are considered as replicates one could include the batch as a factor (as you suggest
below), but if they contain different tumour classes one could not separate the dmso effect from the
"tomour" class effect.

The tissues samples (normal and tumour) are probably from different subjects and will show strong
differences per se. Maybe one get some estimates for the impact of the batch by using a mixed effects model
with each sample as random effect and the batch as fixed effect. 

something like lme(response ~ batch, data=d, rand = ~ 1|sample)

I'm not sure about this, it's just an idea ...

Anyway, I'd pre-process (normalize) all samples together, otherwise there'll certainly be a batch effect.

	kind regards,

	Arne

> -----Original Message-----
> From: bioconductor-bounces@...
> [mailto:bioconductor-bounces@...]On Behalf Of 
> Adaikalavan
> Ramasamy
(Continue reading)

Darlene Goldstein | 1 Dec 13:21 2004
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Re: normalisation or analysis with batch effects


Hi, I just wanted to mention that even if you do normalize all the chips
together, you are still likely to see the 'batch' (or 'block') effects.  To try
to assess the extent of the problem, you might cluster the samples and see if
you get samples from the same batch clustering together.

Best regards, Darlene

-------------------

Hello,

the 11 tumour sampel are considered as biological replicates, or are these split
into different tumour classes?

We've had a similar problem. Our data was generated in three different
laboratories, each having slightly different protocols, but within each lab we
had the same factors (the same doses of a drug).

I guess, if the tumours are considered as replicates one could include the batch
as a factor (as you suggest below), but if they contain different tumour classes
one could not separate the dmso effect from the "tomour" class effect.

The tissues samples (normal and tumour) are probably from different subjects and
will show strong differences per se. Maybe one get some estimates for the impact
of the batch by using a mixed effects model with each sample as random effect
and the batch as fixed effect.

something like lme(response ~ batch, data=d, rand = ~ 1|sample)

(Continue reading)

Dr. Ir. B. van Breukelen | 1 Dec 13:22 2004
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Limma and limmaGUI with Imagene files, problems/bugs report

Dear limma users and developers,

At our laboratory we analyze our MA data using limma. Currently we have
created a dedicated array on which the same set of genes is spotted three
times on one slide. Actually it is one design spotted three times. In
Imagene you can now create a META gid for (in this case) the 4*4 grids. This
grid you call grid A.. Then you can copy it several times (thereby creating
metagrid B and C). You then end up after quantification with a large imagene
file having the information of the three metagrids: (its like having three
slides on one slide!)
e.g.
Field	GridRow	GridCol	SpotRow	SpotCol	ID
A	1		1		1		1		Pp11
A	1		1		1		2		Pp12
..............
A	4		4		17		17		P..
B	1		1		1		1		Pp11
B	1		1		1		2		Pp12
..............
B	4		4		17		17		P..
C	1		1		1		1		Pp11
C	1		1		1		2		Pp12
..............
C	4		4		17		17		P..

When loading these files in either limma and limmaGUI only the A Field is 
read. Not the values belonging to the B and C metagrid (which are the
replicates). 
Is there a simple way to solve this problem ? Or do I have to cut these
files into three parts ?
(Continue reading)

STKH (Steen Krogsgaard | 1 Dec 13:54 2004

RE: Limma and limmaGUI with Imagene files, problems/bugs report

Hi,

we routinely analyze Imagene files with BioC, so perhaps I can answer
some of your problems.

First, you have to define one metagrid for all your spots, BioC won't
understand fields. We have a 4x6 grid spotted twice on the slides, so we
have defined a 4x12 metagrid. I guess you can modify your imagene output
text files in e.g. excel to cope with the grid problem, but I find that
tedious. So define your grid in Imagene once and for all.

readTargets: I do it exactly the way you describe, first readTargets and
the matrix. Is that a problem? It's just two lines of code...

Spottypes: Be sure that the heading of your ID column in the spottypes
file is "Gene ID" (exact spelling but without quotes), then
controlStatus (which I assume you meant when you wrote controlTypes)
will match to the right column in RG (RG <at> genes <at> Gene ID).

Hope this helps
Steen

-----Original Message-----
From: bioconductor-bounces@...
[mailto:bioconductor-bounces@...] On Behalf Of
Dr. Ir. B.
van Breukelen
Sent: 1. december 2004 13:23
To: bioconductor@...
Subject: [BioC] Limma and limmaGUI with Imagene files, problems/bugs
(Continue reading)

Brian K Smith | 1 Dec 16:48 2004
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Re: BioConductor Deployment at a large site, suggestions?


>Your answer most likely would be solved by one of the sections in the FAQ,
>"Downloading All Packages From A Repository".

Unfortunately, I had looked at the FAQ, and it didn't help much,
probably due to my unfamiliarity with the package.  The list gets me
the directories for reposTools, most of which are permission denied when
trying to browse and d/l the .tar.gz directly.

It also doesn't tell me all the packages and dependencies needed for the
"default" install of affy, cdna, and exprs.  Thus every time I upgrade the
package it's far more work than any other R package I've ever encountered,
as I have to figure out what all I need to install in what order.  Thus,
between that and not wanting to hit bioconductor.org 100 times for 100
machines, I upgrade BioConductor rarely.

Perhaps if I was an R guru this would be clear, but I'm a sys admin so
I'm between the simple single user who just wants getBioC() and be done,
and someone who wants their own repository of all the possible packages.
I know just enough to install and basic test R and packages, though I
would love to learn more R, but due to workload, I just don't have time.

I would like an ordered list of packages and dependencies for the default
install into a typical R install.  Thus, I could then script this so
when I need to kickstart install a machine the entire process gets done
in 30 minutes and I have a machine that looked the same as it did before.

Though the smaller ordered R CMD INSTALL list would be ideal, I think
the reposTools and getBioC combined with an R BATCH may work.  I'll
look into it and probably contact you or Robert off list.
(Continue reading)

hrishikesh deshmukh | 1 Dec 16:47 2004
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Perl interface

Hi All,

How can one connect to R using Perl, is RSPerl the
only way?

Thanks in advance.

Hrishi
Jean Yee Hwa Yang | 1 Dec 17:03 2004
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Re: layout for maQualityPlots

Hi,

Try the following:

tmp <- layout(matrix(c(16, 1, 2, 2, 16, 0, 3, 3, 16, 4, 6, 6,
            16, 5, 7, 7, 16, 8, 10, 11, 16, 9, 10, 11, 16, 12, 14, 14, 16,
            13, 15,15), 4, 8), height = c(1, 10, 5, 5), width = c(11,
            2, 5, 1.5, 5, 1.5, 5, 1.5))

layout.show(tmp)

I think help(layout) have sufficient information.

Cheers

Jean

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 Jean Yee Hwa Yang			 jean@...
 Lung Biology Center, 		           Tel: (415) 476-3368
 University of California,		   Fax: (415) 476-6014
 500 Parnassus Avenue, MU 420-W,  San Francisco, CA 94143-0560
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On Mon, 29 Nov 2004, NATALIA F TCHETCHERINA wrote:

> Hello,
> I would like to modify 'maQualityPlots'. I would like to get Spatial plots of
> 'maGb','maGf' instead 'qpDotPlots'. One of things that I need to change is  :
> layout(matrix(c(14, 1, 2, 2, 14, 0, 3, 3, 14, 4, 6, 6, 
(Continue reading)

James W. MacDonald | 1 Dec 17:42 2004
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Re: Re: normalisation or analysis with batch effects

>-----Original Message-----
>From: bioconductor-bounces at stat.math.ethz.ch
>[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of
>Adaikalavan
>Ramasamy
>Sent: 30 November 2004 23:51
>To: BioConductor mailing list
>Cc: Andrea Pellagatti
>Subject: [BioC] normalisation or analysis with batch effects
>
>
>Dear list,
>
>If the following question has been asked before, I do apologise in
>advance and hope someone can point to the relevant thread. Otherwise I
>would appreciate some thoughts and pointers to this problem.
>Thank you.
>
>
>Problem : My collaborator (cc-ed here) has performed hybridisation for
>11 tumour and 40 normal samples on Affymetrix HGU-133Av2
>(contains ~55k
>probesets) chips. He had hybridised about half of the samples when he
>realised he needed more Affymetrix chips.
>
>The second batch of chips arrived with the instruction to add DMSO in
>the hybridisation cocktail, which he followed. The first batch did not
>have such instruction. Therefore we believe that the two
>batches are not

(Continue reading)

Christopher, Neil (NIH/NCI | 1 Dec 18:09 2004
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aCGH modify plotting method

Hello,

I am trying to use the aCGH package to find and plot copy number.  I would
like to modify the function plotHmmStates so that I can control the yScale.
However, I cannot find the source code for this function.  It is usually in
the R directory under the package folder.  However, there is only an RDX and
RDB file.  Are these files compressed archives of the code? If so, how can I
access and change the code?

Thanks,
Neil
Yanqin Yang | 1 Dec 18:29 2004
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Re: problem with hexbin

Hi Agens,

Thanks for your kindly help! I downloaded the hexbin version 1.0.10 at the website you provided. I got the
following error messages.

> maQualityPlots(mraw)
Loading required package: hexbin 
NOTA BENE: This is is an outdated version of the 'hexbin' package.
 It is known to have bugs ``by design''.
 *Strongly* consider using the new 'hexbin' version instead!!
Error in devga(paste("png:", filename, sep = ""), width, height, pointsize,  : 
        unable to start device devga
In addition: Warning message: 
Unable to open file `diagPlot.C:PROGRA~1/R/rw2000/library/marray/swirldata/swirl.1.png' for
writing 

Thanks for your help!

Yanqin

		
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