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Question: beadarray: summarizing iScan data is not working
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gravatar for S. K.
7 months ago by
S. K.0
Germany, Heidelberg
S. K.0 wrote:

Hello,

I am trying to read Illumina HT12-v4 beadarrays with beadarray that were scanned with an iScan system. All necessary files are residing in the current working directory and I am not using a sample file.

library(beadarray)
processSwathData()
ExpBData <- readIllumina(illuminaAnnotation = "Humanv4")
ExpSetData <- summarize(ExpBData,useSampleFac = T)

Summarizing seems to work until the annotation step... then I get the following error message:

Making  summary object
Annotating control probes using package illuminaHumanv4.db Version:1.26.0

Error in value[[3L]](cond) : duplicate row.names: 200647550006
  AnnotatedDataFrame 'initialize' could not update varMetadata:
  perhaps pData and varMetadata are inconsistent?

Removing the useSampleFacs argument to summarize makes the error go away, but then I get an object that has separate entries for each Swath - so 24 "chips" instead of 12.

Can somebody point me in the right direction on how to get correct results?

Thanks,

Simon

R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] illuminaHumanv4.db_1.26.0 org.Hs.eg.db_3.4.0        AnnotationDbi_1.36.2     
 [4] IRanges_2.8.2             S4Vectors_0.12.2          beadarray_2.24.0         
 [7] ggplot2_2.2.1             Biobase_2.34.0            BiocGenerics_0.20.0      
[10] illuminaio_0.16.0        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10         XVector_0.14.1       magrittr_1.5         GenomicRanges_1.26.4
 [5] zlibbioc_1.20.0      munsell_0.4.3        colorspace_1.3-2     stringr_1.2.0       
 [9] GenomeInfoDb_1.10.3  plyr_1.8.4           tools_3.3.3          grid_3.3.3          
[13] base64_2.0           gtable_0.2.0         DBI_0.6-1            lazyeval_0.2.0      
[17] openssl_0.9.6        digest_0.6.12        tibble_1.3.0         reshape2_1.4.2      
[21] bitops_1.0-6         RCurl_1.95-4.8       memoise_1.0.0        RSQLite_1.1-2       
[25] limma_3.30.13        stringi_1.1.5        BeadDataPackR_1.26.0 scales_0.4.1
ADD COMMENTlink written 7 months ago by S. K.0

Just a wild guess but might be related to another problem of mine due to longer chip identifiers since last October:

beadarray: readIllumina with sample sheet broken due to Illumina switching to 12 digit chip identifiers

ADD REPLYlink written 7 months ago by S. K.0
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