R help - May 2012 - File format for single channel analysis of Agilent microarray data in Limma?

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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Please ask BioC related questions on the BioC mailing list.

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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> View this message in context:
http://r.789695.n4.nabble.com/File-format-for-single-channel-analysis-of-Agilent-microarray-data-in-Limma-tp4631061.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Yes, I did that in the end.

Thanks,

Parisa

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