[BioC] About beadarray normaliseIllumina() warning messages

[Matt Ritchie]

Hi Elliot,

If you re-run the read command below with 'Detection = "Detection"' you
should avoid the first message.  You'll still get the warning message from
normaliseIllumina() because the the Detection values aren't passed onto the
LumiBatch object in the current code.  It is my understanding that the
detection values aren't used in vst, so you don't need to worry about this
warning message.

Best wishes,

Matt

> Hi Alice,
> 
> When I added the detection="Detection"as you suggested
> as in,
> 
>> BSData <- readBeadSummaryData( dataFile,
>                                skip = 7,
>                                columns = list( exprs = "AVG_Signal",
>                                                se.exprs = "BEAD_STDEV",
>                                                NoBeads = "Avg_NBEADS",
>                                                detection = "Detection"
>                                              ),
>                               annoPkg = "lumiRatV1"
>                               )
> 
> 
>  I now get the following error message:
>> Did not find a slot called : detection
> 
> This is where I am confused a bit. You see, according the
> readBeadSummaryData
> help file, the default slot name is 'Detection' not 'detection',
> however, the call to
>> BSData.lumi <- normaliseIllumina(BSData, method = "quantile",
> transform = "vst")
> is looking for the slot name 'detection', which doesn't exist because
> readBeadSummaryData()
> wants the slot name to be 'Detection'.
> 
> Is there a way to rename the slot name in the BSData object from
> 'Detection' to 'detection'?
> 
> Thanks for your help!
> 
> Elliot
> 
> Johnstone, Alice wrote:
>> 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.