[BioC] beadarray error: Did not find a slot called : se.exprs

[Matt Ritchie]

Dear Yogi,

The slot that stores the standard errors for each bead type has recently had
a name change from BeadStDev -> se.exprs.

If you run the command from your original email using the current release
version of beadarray (1.6.0), it should work fine, while the command you
tried in your second email will work in the old release (beadarray 1.4.0) as
you have noticed.

Best wishes,

Matt 

> Further to that,
> 
>> BSData2 = readBeadSummaryData("iltp1155_Sample_Gene_Profile.csv",
> + skip = 7, columns = list(exprs ="AVG_Signal", BeadStDev = "BEAD_STDEV",
> NoBeads = "Avg_NBEADS"), sep = ",")
> 
> seems to work fine...
> 
>  -----Original Message-----
> From: Yogi Sundaravadanam
> Sent: Wednesday, 31 October 2007 4:15 PM
> To: bioconductor
> Subject: [BioC] beadarray error: Did not find a slot called : se.exprs
> 
> Dear all,
> 
>  
> 
> I am trying to read a file in R using beadarray package but I seem to
> get an error that says
> 
> ³Did not find a slot called : se.exprs²
> 
>  
> 
> This is what I did
> 
> BSData = readBeadSummaryData("ILTP1086_Sample_Gene_Profile.csv",
> 
> + skip = 7, columns = list(exprs ="AVG_Signal", se.exprs = "BEAD_STDEV",
> NoBeads = "Avg_NBEADS"), sep = ",")
> 
>  
> 
> Am I doing something horribly wrong? I spent the whole afternoon trying
> to figure out what the problem is, and it could just be a trivial thing
> but I would be grateful for any insights!
> 
>  
> 
> Thanks heaps
> 
> Yogi
> 
>  
> 
> Sessioninfo()
> 
>> sessionInfo()
> 
> R version 2.5.1 (2007-06-27)
> 
> x86_64-unknown-linux-gnu
> 
>  
> 
> locale:
> 
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.U
> TF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-
> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_ID
> ENTIFICATION=C
> 
>  
> 
> attached base packages:
> 
> [1] "grid"      "tools"     "stats"     "graphics"  "grDevices" "utils"
> 
> [7] "datasets"  "methods"   "base"
> 
>  
> 
> other attached packages:
> 
>    beadarray beadarraySNP  quantsmooth      lodplot     quantreg
> SparseM
> 
>      "1.4.0"      "1.2.0"      "1.2.0"        "1.1"       "4.10"
> "0.74"
> 
>         affy       affyio  geneplotter      lattice     annotate
> Biobase
> 
>     "1.14.2"      "1.4.1"     "1.14.0"    "0.15-11"     "1.14.1"
> "1.14.1"
> 
>        limma
> 
>     "2.10.5"
> 
>  
> 
>  
> 
> 
> 
> [[alternative HTML version deleted]]
> 
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