[BioC] .CEL file
James W. MacDonald
jmacdon at uw.edu
Thu Mar 27 22:48:39 CET 2014
BRB array tools uses R and bioconductor tools to process the celfiles.
The only thing it does in Excel is to make comparisons after the arrays
have been processed.
And as I said before, I can't help you with this. There are any number
of ways to process raw Affymetrix data that are fast, free and already
in existence. This is a solved problem, so if you want to solve it
again using Excel, then have at it. But I wouldn't expect that many
people want to spend much time helping you.
On Thursday, March 27, 2014 5:39:32 PM, prabhakar ghorpade wrote:
> Did You tried BRB Array Tool. It uses Excel.
> Dr. Ghorpade Prabhakar B.
> PhD Scholar ( Veterinary Biochemistry),
> Bareilly, U.P.,
> On Friday, 28 March 2014 2:35 AM, James W. MacDonald <jmacdon at uw.edu> wrote:
> OK, well in that case good luck! I don't think I can help you with that,
> but maybe some of the functions I pointed out will be helpful.
> On 3/27/2014 4:59 PM, prabhakar ghorpade wrote:
>> Thanks for reply james,
>> I want to create .CEL file which looks like file from
>> machine but with smaller data set. I am interested to see if I can
>> perform same analysis in excel as in R.
>> /Dr. Ghorpade Prabhakar B./
>> /PhD Scholar ( Veterinary Biochemistry),/
>> /Bareilly, U.P.,/
>> On Friday, 28 March 2014 2:19 AM, James W. MacDonald <jmacdon at uw.edu>
>> Hi Prabhakar,
>> On Thursday, March 27, 2014 4:32:27 PM, prabhakar ghorpade wrote:
>>> How can I view .CEL file? Is it possible to make dummy .CEL file
>> for analysis?
>> Can you expand on this a bit? What exactly are you trying to do?
>> The celfile format is quite complicated, so creating a dummy file is
>> likely to be more work than just getting some data from say, GEO or
>> ArrayExpress and doing whatever you want.
>> As for viewing a celfile, depending on what you mean by that, there are
>> multiple options.
>> 1.) If the celfile is text, you can just send it to stdout using 'cat'.
>> Or if it is binary you can use the celfile converter to make it text,
>> and then use cat
>> 2.) You could use the various functions in affxparser (readCel,
>> readCelHeader, readCelIntensities, etc).
>> 3.) You could use functions in affyio, either directly or via the affy
>> package. Or if the array you care about is a more modern version, then
>> you could use oligo and the respective pdInfoPackage. Or probably use
>> some functions in xps that I don't know about.
>>> Dr. Ghorpade Prabhakar B.
>>> PhD Scholar ( Veterinary Biochemistry),
>>> Bareilly, U.P.,
>>> [[alternative HTML version deleted]]
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>> James W. MacDonald, M.S.
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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