[R] File format for single channel analysis of Agilent microarray data in Limma?

[Uwe Ligges]

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Best,
Uwe Ligges

On 23.05.2012 11:44, Parisa wrote:
> Hi,
>
> I am following the protocol outlined here for analysis of single channel
> Agilent microarray data:
>
> http://matticklab.com/index.php?title=Single_channel_analysis_of_Agilent_microarray_data_with_Limma
>
> I keep getting the following error message when using Limma's read.maimages
> function to load my data into an RGList object:
>
> Error in RG[[a]][, i]<- obj[, columns[[a]]] :
>    number of items to replace is not a multiple of replacement length
>
> I think this may be due to my Agilent raw data txt files being in the wrong
> format. I am having difficulty finding an example Agilent feature extraction
> raw data txt file online to compare it to. I have attached a screen shot of
> one of the files I am using below (as the file itself is too large to
> upload). I would appreciate if someone could let me know if it is in the
> correct format, and if not then what format it should be in to prevent the
> above error message from coming up.
>
> Thank you,
>
> Parisa
>
> http://r.789695.n4.nabble.com/file/n4631061/Screen_shot_2012-05-23_at_10.41.56.png
> Screen_shot_2012-05-23_at_10.41.56.png
>
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