[BioC] Lumi package: control data for background correction

Tue Jan 15 17:47:15 CET 2008

Hi Merja,

We have added some control probe related functions in the developing version
of lumi. Now, you can easily input and plot the control probe information
output by BeadStudio. Related functions include:
"getControlData"
"addControlData2lumi"
"plotControlData"
"plotHousekeepingGene"
"plotStringencyGene"
We will add more detailed description in the vignette later. As it is still
under improvement, any suggestions are welcome.

You can get the source code from:
http://www.bioconductor.org/packages/2.2/bioc/html/lumi.html

Pan

On 1/15/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Message: 1
> Date: Mon, 14 Jan 2008 12:07:49 +0100
> From: "merja matilainen" <merja.matilainen at uni.lu>
> Subject: [BioC] Lumi package: control data for background correction
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <46B6E4B75821C449868D25354BE0839F84628B at solo.uni.lux>
> Keywords: disclaimer
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Hi!
> 
> I have Illumina data for analysis that is produced with BeadStudio v3. It is
> not background corrected and also not normalized. I wanted to try the lumi
> package and I found a previous posting to the mailing list describing how to
> read in the control data from a separate file
> http://article.gmane.org/gmane.science.biology.informatics.conductor/15391/mat
> ch=gordon+background+correction+lumi
> 
> I did the same (as far as I can tell)
>> rawX=lumiR("raw_data.txt")
>> controlgp=lumiR("qcinfo.txt")
>> rawX at controlData=as.data.frame(exprs(controlgp))
>> rawXbgc=lumiB(rawX,method="bgAdjust")
> 
> Here is what I have in rawX
>> exprs(rawX[1:5,1:8])
>         1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B
> 1881436009_C 1881436049_A 1881436049_B
> 20605      270.30210    252.15860    271.25070    277.39090    249.06970
> 221.26020     223.3545    231.69390
> 3450747    483.33750    423.05290    460.44330    547.50350    462.51610
> 439.66790     408.1301    433.04090
> 3060450    620.23050    621.86890    626.29790    703.47220    562.79860
> 483.12060     523.9857    571.69780
> 870131      78.45721     71.16602     67.74918     75.95979     75.14289
> 74.56358      80.1152     74.99714
> 5310368     90.98277     79.14721     82.17856     85.82687     89.79446
> 81.63494      80.4482     74.59328
> 
> 
> Here is part of my @controlData
>> rawX at controlData
>                     1881436004_A 1881436004_B 1881436004_C 1881436004_D
> 1881436004_E 1881436004_F 1881436009_A
> BIOTIN                6683.65000   6280.45700   5796.20100   6058.32500
> 5540.00200   6039.07700   6612.78700
> CY3_HYB              13238.52000  12945.04000  12741.06000  12797.29000
> 11272.87000  12798.53000  12288.96000
> HIGH_STRINGENCY_HYB  31363.13000  33693.30000  31494.96000  32456.38000
> 29554.45000  31253.40000  29861.95000
> HOUSEKEEPING         20446.56000  19445.20000  19390.52000  19781.67000
> 18907.65000  19454.81000  20602.37000
> LABELING                85.73669     78.42913     82.58459     79.09451
> 80.69878     80.78196     90.47139
> LOW_STRINGENCY_HYB   13349.75000  12996.49000  12820.47000  12872.48000
> 11340.68000  12900.72000  12363.55000
> NEGATIVE                84.07156     80.37030     83.57912     79.34184
> 80.80109     78.84014
> 
> So why does lumiB then subtract CY3_HYB from the original values because that
> seems to have happened here?????
>> exprs(rawXbgc[1:5,1:8])
>         1881436004_A 1881436004_B 1881436004_C 1881436009_A 1881436009_B
> 1881436009_C 1881436049_A 1881436049_B
> 20605      -12968.22    -12692.88    -12469.81    -12011.57    -13004.72
> -12574.24    -11326.32    -10950.92
> 3450747    -12755.18    -12521.99    -12280.62    -11741.46    -12791.27
> -12355.83    -11141.54    -10749.57
> 3060450    -12618.29    -12323.17    -12114.76    -11585.49    -12690.99
> -12312.38    -11025.68    -10610.91
> 870131     -13160.06    -12873.87    -12673.31    -12213.00    -13178.65
> -12720.94    -11469.55    -11107.61
> 5310368    -13147.54    -12865.89    -12658.88    -12203.13    -13164.00
> -12713.87    -11469.22    -11108.02
> 
> If you have trouble reading the columns, here an example with the first
> datapoint: 270.30210-13238.52000 = -12968.22
> 
> What should have happened is subtraction of average value of negative control
> values so sth like 80.
> 
> Here is the session info if that is useful:
> 
> R version 2.6.1 (2007-11-26)
> i386-apple-darwin8.10.1
> 
> locale:
> C
> 
> attached base packages:
> [1] tools     stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>  [1] lumi_1.4.0           annotate_1.16.1      xtable_1.5-2
> AnnotationDbi_1.0.6  RSQLite_0.6-4
>  [6] DBI_0.2-4            mgcv_1.3-29          affy_1.16.0
> preprocessCore_1.0.0 affyio_1.6.1
> [11] Biobase_1.16.2
> 
> 
> Could this be sth wrong with my file? Anyone able to point me to the problem?
> 
> Thanks!
> 
> Merja
> ###########################################
> 
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---------------------------------------------------
Pan Du, PhD
Research Assistant Professor
Robert H. Lurie Comprehensive Cancer Center
Northwestern University
676 ST Clair St., #1200
Chicago, IL 60611
Office (312)695-4781
dupan at northwestern.edu