Dear all,
I have searched through the bioconductor ducument and this mailing
list, but
could not find a general guidance about how to correct background in
cDNA
array data. I have imported my data (GPR files from GenePix) using
functions from marray. Now what are the available methods for
background
correction before normalization? Any suggestions/experience is very
much
appreciated.
Regards,
Qi Zhang
Did you want to write your own background correction method? The
normalization routines in marray and limma do background correction.
--Naomi
At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote:
>Dear all,
>
>I have searched through the bioconductor ducument and this mailing
list, but
>could not find a general guidance about how to correct background in
cDNA
>array data. I have imported my data (GPR files from GenePix) using
>functions from marray. Now what are the available methods for
background
>correction before normalization? Any suggestions/experience is very
much
>appreciated.
>
>Regards,
>
>Qi Zhang
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111
Naomi, thanks for your reply. I do not intent to write my own mathod.
I
took the default option when read in the gpr file using read.GenePix,
so I
assume the background correction was done by "substraction". I
remember it
from somewhere that the "substraction" may introduce additional
variance
depends on the algorithm of the background estimation (from the iamge
analysis software). Is the "substraction" the only bg correction
method in
marray? limma has more options, but I have no idea about the
advantage or
disadvantage of them. Any suggestions will be very helpful.
Thanks.
Qi
-----Original Message-----
From: Naomi Altman [mailto:naomi@stat.psu.edu]
Sent: Wednesday, October 26, 2005 7:42 PM
To: Zhang, Qi; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] background correction with cDNA array data
Did you want to write your own background correction method? The
normalization routines in marray and limma do background correction.
--Naomi
At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote:
>Dear all,
>
>I have searched through the bioconductor ducument and this mailing
list,
but
>could not find a general guidance about how to correct background in
cDNA
>array data. I have imported my data (GPR files from GenePix) using
>functions from marray. Now what are the available methods for
background
>correction before normalization? Any suggestions/experience is very
much
>appreciated.
>
>Regards,
>
>Qi Zhang
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111
You can also have a look at the recent book: "Bioinformatics and
Computational Biology Solutions Using R and Bioconductor"
from Robert Gentleman, Vince Carey, Wolfgang Huber, Rafael Irizarry
and
Sandrine Dudoit.
http://www.bioconductor.org/pub/docs/mogr/
They have done a great job.
David
On Oct 27, 2005, at 5:01, Qi.Zhang at astrazeneca.com wrote:
> Naomi, thanks for your reply. I do not intent to write my own
mathod.
> I
> took the default option when read in the gpr file using
read.GenePix,
> so I
> assume the background correction was done by "substraction". I
> remember it
> from somewhere that the "substraction" may introduce additional
> variance
> depends on the algorithm of the background estimation (from the
iamge
> analysis software). Is the "substraction" the only bg correction
> method in
> marray? limma has more options, but I have no idea about the
> advantage or
> disadvantage of them. Any suggestions will be very helpful.
>
> Thanks.
>
> Qi
>
> -----Original Message-----
> From: Naomi Altman [mailto:naomi at stat.psu.edu]
> Sent: Wednesday, October 26, 2005 7:42 PM
> To: Zhang, Qi; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] background correction with cDNA array data
>
>
> Did you want to write your own background correction method? The
> normalization routines in marray and limma do background correction.
>
> --Naomi
>
> At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote:
>> Dear all,
>>
>> I have searched through the bioconductor ducument and this mailing
>> list,
> but
>> could not find a general guidance about how to correct background
in
>> cDNA
>> array data. I have imported my data (GPR files from GenePix) using
>> functions from marray. Now what are the available methods for
>> background
>> correction before normalization? Any suggestions/experience is
very
>> much
>> appreciated.
>>
>> Regards,
>>
>> Qi Zhang
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
> Naomi S. Altman 814-865-3791 (voice)
> Associate Professor
> Dept. of Statistics 814-863-7114 (fax)
> Penn State University 814-865-1348
(Statistics)
> University Park, PA 16802-2111
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
Naomi, thanks for your reply. I do not intent to write my own mathod.
I
took the default option when read in the gpr file using read.GenePix,
so I
assume the background correction was done by "substraction". I
remember it
from somewhere that the "substraction" may introduce additional
variance
depends on the algorithm of the background estimation (from the iamge
analysis software). Is the "substraction" the only bg correction
method in
marray? limma has more options, but I have no idea about the
advantage or
disadvantage of them. Any suggestions will be very helpful.
Thanks.
Qi
-----Original Message-----
From: Naomi Altman [mailto:naomi@stat.psu.edu]
Sent: Wednesday, October 26, 2005 7:42 PM
To: Zhang, Qi; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] background correction with cDNA array data
Did you want to write your own background correction method? The
normalization routines in marray and limma do background correction.
--Naomi
At 04:51 PM 10/26/2005, Qi.Zhang at astrazeneca.com wrote:
>Dear all,
>
>I have searched through the bioconductor ducument and this mailing
list,
but
>could not find a general guidance about how to correct background in
cDNA
>array data. I have imported my data (GPR files from GenePix) using
>functions from marray. Now what are the available methods for
background
>correction before normalization? Any suggestions/experience is very
much
>appreciated.
>
>Regards,
>
>Qi Zhang
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor
Naomi S. Altman 814-865-3791 (voice)
Associate Professor
Dept. of Statistics 814-863-7114 (fax)
Penn State University 814-865-1348
(Statistics)
University Park, PA 16802-2111
On 10/26/05 11:01 PM, "Qi.Zhang at astrazeneca.com" <qi.zhang at="" astrazeneca.com="">
wrote:
> Naomi, thanks for your reply. I do not intent to write my own
mathod. I
> took the default option when read in the gpr file using
read.GenePix, so I
> assume the background correction was done by "substraction". I
remember it
> from somewhere that the "substraction" may introduce additional
variance
> depends on the algorithm of the background estimation (from the
iamge
> analysis software). Is the "substraction" the only bg correction
method in
> marray? limma has more options, but I have no idea about the
advantage or
> disadvantage of them. Any suggestions will be very helpful.
All the bioconductor packages contain extensive help, and limma has
some of
the best help files available. Simply reading the help for the
backgroundCorrect function in limma gives you a rather concise
description
of the various options available. There are also references given
which you
can certainly pull for more information. If contemplating using
limma, a
required read is the relevant section(s) of the limma user guide. All
that
said, there is nothing wrong with trying each method and then plotting
your
data to get a feel for what is really going on with your data.
Sean
I'm not sure if this can help you.
I also was interested in methods for background subtraction, and most
of all in
understanding if or not subtract the background.
The only paper I found about last topic is:
"When should one subtract background fluorescence in two color
microarrays", by
Parmigianini at. al.
Give a look, may be can help you.
Regards
Giuseppe
Quoting Qi.Zhang at astrazeneca.com:
> Dear all,
>
> I have searched through the bioconductor ducument and this mailing
list, but
> could not find a general guidance about how to correct background in
cDNA
> array data. I have imported my data (GPR files from GenePix) using
> functions from marray. Now what are the available methods for
background
> correction before normalization? Any suggestions/experience is very
much
> appreciated.
>
> Regards,
>
> Qi Zhang
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
