It's going to be tough to run neqc() without control probes (in fact I was
under the impression that neqc was only for Illumina arrays, but I could be
wrong).  It's a neat dataset for sure, but if I look into it (I've been
monkeying around with GEO and Agilent/Affy/Illumina/RNAseq conversions a
lot lately), I get the feeling that you could have issues with processing
it:

> library(GEOquery)
> Mori <- getGEO('GSE21815')[[1]]
Found 1 file(s)
GSE21815_series_matrix.txt.gz
Using locally cached version: /tmp/RtmpZwVlZL/GSE21815_series_matrix.txt.gz
Using locally cached version of GPL6480 found here:
/tmp/RtmpZwVlZL/GPL6480.soft
> grep('control', fvarLabels(Mori), ignore.case=TRUE, value=TRUE)
[1] "CONTROL_TYPE"
> table(fData(Mori)$CONTROL_TYPE)

FALSE
41000

I could certainly be wrong, but this would seem to be a problem if you want
to use neqc().  Hopefully Wei Shi or Gordon Smyth or someone who knows
better will chime in...


On Thu, Dec 8, 2011 at 5:14 AM, Femke [guest] <guest@bioconductor.org>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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
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> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
If people do not believe that mathematics is simple,
it is only because they do not realize how complicated life is. John von
Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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