[BioC] Background correction with neqc

[Wei Shi]

Dear Femke,

Your R is 2 years old. Could you update your R and limma to the latest version and then rerun your code?

We have successfully applied neqc function to the Agilent one-color array data which contains ~100 negative control probes (we used raw data). But I can't see any reason why it did not work on the GEO data.

Cheers,
Wei 


On Dec 9, 2011, at 12:14 AM, Femke [guest] wrote:

> 
> Dear All,
> 
> I downloaded gene expression profiles of 132 laser microdissected colorectal cancer tissues from GEO (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE21815), from this dataset I would like to analyze the differential expression between the last 32 tumor and 9 normal tissues. I have no experience with this. I think the array is the single-color type.
> 
> I loaded the data into R, and now I would like to run the function neqc() for background correction and normalization, however I am getting an error. Below I put my commands and the error statement. What am I doing wrong? Is the problem in making the EListRaw or the second step? What is alpha? I tried to find answers on the web but failed.
> 
> Many thank!
> Femke
> 
> library(limma)
> 
> read.maimages(files=c("GSM543223.txt","GSM543224.txt","GSM543225.txt","GSM543226.txt","GSM543227.txt","GSM543228.txt","GSM543229.txt","GSM543230.txt","GSM543231.txt","GSM543232.txt","GSM543233.txt","GSM543234.txt","GSM543235.txt","GSM543236.txt","GSM543237.txt","GSM543238.txt","GSM543239.txt","GSM543240.txt","GSM543241.txt","GSM543242.txt","GSM543243.txt","GSM543244.txt","GSM543245.txt","GSM543246.txt","GSM543247.txt","GSM543248.txt","GSM543249.txt","GSM543250.txt","GSM543251.txt","GSM543252.txt","GSM543253.txt","GSM543254.txt","GSM543255.txt","GSM543256.txt","GSM543257.txt","GSM543258.txt","GSM543259.txt","GSM543260.txt","GSM543261.txt","GSM543262.txt","GSM543263.txt"), source="agilent", names=c("CRC_101","CRC_102","CRC_103","CRC_104","CRC_105","CRC_106","CRC_107","CRC_108","CRC_109","CRC_110","CRC_111","CRC_112","CRC_113","CRC_114","CRC_115","CRC_116","CRC_117","CRC_118","CRC_119","CRC_120","CRC_121","CRC_122","CRC_123","CRC_124","CRC_125","CRC_126","CRC_127","CRC_128","CRC
> _129","CRC_130","CRC_131","CRC_132","normal_1","normal_2","normal_3","normal_4","normal_5","normal_6","normal_7","normal_8","normal_9"), channels=1) -> data
> 
> 
> neqc(data$E, status=data$genes$ControlType)
> 
> Error in if (alpha <= 0) stop("alpha must be positive") : 
>  missing value where TRUE/FALSE needed
> 
> 
> -- output of sessionInfo(): 
> 
> R version 2.10.1 (2009-12-14) 
> x86_64-pc-linux-gnu 
> 
> locale:
> [1] C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] limma_3.2.1
> 
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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