Hi all,
We've been using Agilent Scanner and Feature Extraction from Agilent.
I'm wondering if there's a way to import these data into limma. Out of
the
three required input files (GAL file, Targets file, Spot-type file),
we only
have GAL file. FE gives us SHP file and a txt file witn compiled list
of
probes and its reading. We are doing 2 color microarray btw.
If you know any detail, please help us.
Also, is it possible to group a certain probes together as one entity
(they
are expected to have the same result)? And is it possible to give a
set of
probes as normalizing set for limma (set ratio to 1-1)?
I've been looking through the manual but could not find any reference
about
Agilent output file.
Thanks all
--
Regards,
Anh Tran
[[alternative HTML version deleted]]
On Mon, Jun 2, 2008 at 6:26 PM, Anh Tran <popophobia at="" gmail.com="">
wrote:
> Hi all,
> We've been using Agilent Scanner and Feature Extraction from
Agilent.
>
> I'm wondering if there's a way to import these data into limma. Out
of the
> three required input files (GAL file, Targets file, Spot-type file),
we only
> have GAL file. FE gives us SHP file and a txt file witn compiled
list of
> probes and its reading. We are doing 2 color microarray btw.
>
> If you know any detail, please help us.
>
> Also, is it possible to group a certain probes together as one
entity (they
> are expected to have the same result)? And is it possible to give a
set of
> probes as normalizing set for limma (set ratio to 1-1)?
Limma offers many options for normalization and choosing probes for
normalization. I would definitely put some thought into the rationale
for using a subset of the probes, though.
> I've been looking through the manual but could not find any
reference about
> Agilent output file.
You'll need to look at the help, also. Look at the help for
read.maimages(). Let us know if that doesn't work by posting the code
you tried, any errors, and of course the output of sessionInfo().
Sean
Hi,
Thanks for the reply. I'm still not quite understand your reply.
1. Does it mean that this feature is not implemented into limma
package yet?
2. I want to import the output after extract the intensity (using
external program) and only use limma for normalization, not the image
file to scan from scratch. Is there a way to manage that?
Thanks again.
Best,
Anh Tran
On Jun 2, 2008, at 5:56 PM, Sean Davis wrote:
> On Mon, Jun 2, 2008 at 6:26 PM, Anh Tran <popophobia at="" gmail.com="">
wrote:
>> Hi all,
>> We've been using Agilent Scanner and Feature Extraction from
Agilent.
>>
>> I'm wondering if there's a way to import these data into limma. Out
>> of the
>> three required input files (GAL file, Targets file, Spot-type
>> file), we only
>> have GAL file. FE gives us SHP file and a txt file witn compiled
>> list of
>> probes and its reading. We are doing 2 color microarray btw.
>>
>> If you know any detail, please help us.
>>
>> Also, is it possible to group a certain probes together as one
>> entity (they
>> are expected to have the same result)? And is it possible to give a
>> set of
>> probes as normalizing set for limma (set ratio to 1-1)?
>
> Limma offers many options for normalization and choosing probes for
> normalization. I would definitely put some thought into the
rationale
> for using a subset of the probes, though.
>
>> I've been looking through the manual but could not find any
>> reference about
>> Agilent output file.
>
> You'll need to look at the help, also. Look at the help for
> read.maimages(). Let us know if that doesn't work by posting the
code
> you tried, any errors, and of course the output of sessionInfo().
>
> Sean
On Mon, Jun 2, 2008 at 10:31 PM, Anh Tran <popophobia at="" gmail.com="">
wrote:
> Hi,
>
> Thanks for the reply. I'm still not quite understand your reply.
>
> 1. Does it mean that this feature is not implemented into limma
package yet?
>
> 2. I want to import the output after extract the intensity (using
external
> program) and only use limma for normalization, not the image file to
scan
> from scratch. Is there a way to manage that?
Hi, Anh. Again, you'll want to read the help for read.maimages. You
can do this by loading the limma package and then typing:
help(read.maimages)
In particular, look at the "source" argument. And, yes, this function
reads the .txt file after feature extraction. If you need a list of
all the functions for which there is help in limma, you can type:
help(package=limma)
Again, if you have further questions, please include the code you
tried, any errors, and for ANY questions to the list, the output from
the sessionInfo() function.
Hope that clarifies.
Sean
> On Jun 2, 2008, at 5:56 PM, Sean Davis wrote:
>
>> On Mon, Jun 2, 2008 at 6:26 PM, Anh Tran <popophobia at="" gmail.com="">
wrote:
>>>
>>> Hi all,
>>> We've been using Agilent Scanner and Feature Extraction from
Agilent.
>>>
>>> I'm wondering if there's a way to import these data into limma.
Out of
>>> the
>>> three required input files (GAL file, Targets file, Spot-type
file), we
>>> only
>>> have GAL file. FE gives us SHP file and a txt file witn compiled
list of
>>> probes and its reading. We are doing 2 color microarray btw.
>>>
>>> If you know any detail, please help us.
>>>
>>> Also, is it possible to group a certain probes together as one
entity
>>> (they
>>> are expected to have the same result)? And is it possible to give
a set
>>> of
>>> probes as normalizing set for limma (set ratio to 1-1)?
>>
>> Limma offers many options for normalization and choosing probes for
>> normalization. I would definitely put some thought into the
rationale
>> for using a subset of the probes, though.
>>
>>> I've been looking through the manual but could not find any
reference
>>> about
>>> Agilent output file.
>>
>> You'll need to look at the help, also. Look at the help for
>> read.maimages(). Let us know if that doesn't work by posting the
code
>> you tried, any errors, and of course the output of sessionInfo().
>>
>> Sean
>
>
