[BioC] About beadarray normaliseIllumina() warning messages

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Thu Jan 10 00:42:12 CET 2008

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
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

* 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    

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)


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

Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
Search the archives:

P Think before you print
This e-mail transmission and any attachments that accompany it may contain information that is privileged, confidential or otherwise exempt from disclosure under applicable law and is intended solely for the use of the individual(s) to whom it was intended to be addressed.
If you have received this e-mail by mistake, or you are not the intended recipient, any disclosure, dissemination, distribution, copying or other use or retention of this communication or its substance is prohibited. If you have received this communication in error, please immediately reply to the author via e-mail that you received this message by mistake and also permanently delete the original and all copies of this e-mail and any attachments from your computer. Thank you.

More information about the Bioconductor mailing list