[BioC] About beadarray normaliseIllumina() warning messages

[Elliot Kleiman]

Hi Matt,

Cool, thanks for the heads-up about not having
to be concerned about those vst detection warning
messages. :)

Cheers,

Elliot

Matt Ritchie wrote:
> 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.
>>>       
>
>
>   


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