[BioC] About beadarray normaliseIllumina() warning messages

[Johnstone, Alice]

You just need to add the detection="Detection" to the list of columns in
the readBeadSummaryData command so that it reads this column of your
data also.

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Elliot
Kleiman
Sent: Thursday, 10 January 2008 11:55 a.m.
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] About beadarray normaliseIllumina() warning messages

Hi BioC list,

In package beadarray, when I call function normaliseIllumina() with
arguments [method = "quantile", transform = "vst"] I get the following
warning messages:

Warning messages:
1: In detectionCall(x.lumi, Th = 0.01, type = "matrix") :
  No detection slot found!
2: In rm(list = c("se.exprs", "detection", "beadNum"), envir = aData) :
  variable "detection" was not found

[Question(s)]:
* Does that mean it's still doing what its supposed to be doing? (Or is
it bailing out returning these warnings messages instead?)
* I am wondering if its safe to simply ignore these warnings?

Here's a snippet of my raw bead summary header-info:
---
Illumina Inc. BeadStudio version 2.3.47
Normalization = none
Array Content = RatRef_12_v1_11222119_A.xml.xml Error Model = none
DateTime = 7/12/2007 12:18 PM Local Settings = en-US

TargetID    MIN_Signal    AVG_Signal    MAX_Signal    NARRAYS    
ARRAY_STDEV    BEAD_STDEV    Avg_NBEADS    Detection
---

For example, when I go to read in my raw bead summary data and vst
transform with quantile normalization, I do:

 > # load packages
 > library(beadarray)
 > library(lumi)
 > library(lumiRatV1)
 > # read-in raw bead summary data
 > # create BSData object
 > BSData <- readBeadSummaryData( dataFile,
                               skip = 7,
                               columns = list( exprs = "AVG_Signal",
                                               se.exprs = "BEAD_STDEV",
                                               NoBeads = "Avg_NBEADS"
                                             ),
                              annoPkg = "lumiRatV1"
                              )
 > # perform lumi vst transformation and quantile normalization  >
BSData.lumi <- normaliseIllumina(BSData, method = "quantile", transform
= "vst")
2008-01-09 13:54:12 , processing array  1 ...
2008-01-09 13:54:21 , processing array  48 Warning messages:
1: In detectionCall(x.lumi, Th = 0.01, type = "matrix") :
  No detection slot found!
2: In rm(list = c("se.exprs", "detection", "beadNum"), envir = aData) :
  variable "detection" was not found

Thank you,

Elliot Kleiman

 > # print sessionInfo
 > sessionInfo()
R version 2.6.1 (2007-11-26)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY=en_US
;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;
LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods 
[8] base    

other attached packages:
 [1] beadarray_1.6.0      geneplotter_1.16.0   lattice_0.17-2     
 [4] maSigPro_1.10.0      lumiRatV1_1.3.1      estrogen_1.8.2     
 [7] vsn_3.2.1            hgu95av2cdf_2.0.0    hgu95av2_2.0.1     
[10] limma_2.12.0         lumi_1.4.0           annotate_1.16.1    
[13] xtable_1.5-2         AnnotationDbi_1.0.6  RSQLite_0.6-4      
[16] DBI_0.2-4            mgcv_1.3-29          affy_1.16.0        
[19] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.2     

loaded via a namespace (and not attached):
[1] KernSmooth_2.22-21 RColorBrewer_1.0-2 grid_2.6.

--
__________________________
MS graduate student
Program in Computational Science
San Diego State University
http://www.csrc.sdsu.edu/

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