[BioC] Get negative control probes in lumiBarnes data set

[Sandra Plancade [guest]]

Hi,

I would like to get the regular and the negative control probes from the Illumina data set "lumiBarnes" in the lumi package. This data set consists of 16 arrays on Illumina chips Human_RefSeq8_v1.

My problem is that the function getControlData returns me only 22 control probes (see code below). I was very surprised (even if I have never worked on these specific chips before), because the number of negative probes on Illumina microarrays is usually between 500 and 1500. 

Thus, I have two questions:

1) How can I find the number of control probes on Human_RefSeq8_v1 chips? (I found it in beadarray for some other type of chips, but not for this one).

2) Do I do the correct procedure to extract the negative control probes? 

Thanks in advance for your help. 

Sandra Plancade



###############################
## This is the code :

library(lumi)
library(lumiBarnes)
data(lumiBarnes)

## Control probes
 getControlData(lumiBarnes)

## I get a 22*16 matrix with colnames (A01,...,B08) corresponding to the 16 samples, and 22 probes. 





 -- output of sessionInfo(): 

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915
 [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

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

other attached packages:
 [1] lumiBarnes_1.3.4     lumi_1.12.4          MASS_7.3-3
 [4] RSQLite_0.9-3        DBI_0.2-5            preprocessCore_1.8.0
 [7] mgcv_1.5-6           affy_1.24.2          annotate_1.24.1
[10] AnnotationDbi_1.8.2  beadarray_1.14.0     Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0   grid_2.10.0     hwriter_1.3     lattice_0.17-26
[5] limma_3.2.3     nlme_3.1-96     tools_2.10.0    xtable_1.5-6


--
Sent via the guest posting facility at bioconductor.org.