Question: background correction of Single colour Agilent Microarrays
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gravatar for ragavendrasamy.b
2.2 years ago by
ragavendrasamy.b0 wrote:

Dear All,

I have been trying to perform background correct for the Agilent Single Color Array 8X60K using Limma

But when i had tried it, i am getting the following response.

> backgroundCorrect(X, method="subtract", offset=0)
Error in backgroundCorrect(X, method = "subtract", offset = 0) : 
  subtractcorrection requires background intensities

However, the .txt file that i have loaded contains the background intensity information.

Please kindly suggest me how i can rectify this error. I intend to take the background corrected data further into Genespring software.

Thanks for your help in advance

Regards,

Ragavendrasamy

ADD COMMENTlink modified 2.2 years ago by Gordon Smyth37k • written 2.2 years ago by ragavendrasamy.b0
Answer: background correction of Single colour Agilent Microarrays
0
gravatar for Gordon Smyth
2.2 years ago by
Gordon Smyth37k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth37k wrote:

Well, you apparently didn't read the background intensities when you read the raw files into R. I can't tell you what you did wrong without seeing the code you used to read and create 'X'.

If you're planning to use Genespring, it does raise the question of why are you background correcting in limma at all? Genespring is perfectly capable of subtracting background itself. (limma on the other hand offers much better background correction and testing methods, although you don't seem to want to use them.)

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Gordon Smyth37k
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