[BioC] Background correction with neqc

Gordon K Smyth smyth at wehi.EDU.AU
Sat Dec 10 07:19:58 CET 2011


Dear Femke,

Please type

   table(data$genes$ControlType)

and tell us the results.

As Tim Triche has pointed out, GEO may not preserve negative control 
probes in the public data and, if not, you obviously cannot use neqc(). 
In the absence of negative control probes, you would instead use

   backgroundCorrect(data,method="normexp")

etc.

Best wishes
Gordon

> Date: Thu,  8 Dec 2011 05:14:37 -0800 (PST)
> From: "Femke [guest]" <guest at bioconductor.org>
> To: bioconductor at r-project.org, femke.simmer at googlemail.com
> Subject: [BioC] Background correction with neqc
>
> 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
>
> --


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