[BioC] AgiMicroRna rmaMicriRna call fails

Thomas Hampton thomas.h.hampton at dartmouth.edu
Thu Sep 2 16:22:52 CEST 2010


Not sure what I am doing wrong.

Any ideas?

Best,

Tom

> sessionInfo()
R version 2.10.0 (2009-10-26)
powerpc-apple-darwin9.8.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] gplots_2.7.4         caTools_1.10         bitops_1.0-4.1
[4] gdata_2.6.1          gtools_2.6.1         AgiMicroRna_1.0.0
[7] preprocessCore_1.8.0 affy_1.24.2          limma_3.2.1
[10] Biobase_2.6.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0 tcltk_2.10.0  tools_2.10.0


> dd.micro=readMicroRnaAFE(targets,verbose=TRUE)
Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_1.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_2.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_3.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_1_4.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_1.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_2.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_3.txt
Read US22502536_251911814270_S01_miRNA-v1_95_May07_2_4.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_1_1.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_1_2.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_1_3.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_1_4.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_2_1.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_2_2.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_2_3.txt
Read kathy martin-J-july-scanrepeat/K.Martin 8x15K  
miRNA_251911814197_S01_miRNA-v1_95_May07_2_4.txt

RGList:
	dd$R:		'gTotalGeneSignal'
	dd$G:		'gTotalProbeSignal'
	dd$Rb:		'gMeanSignal'
	dd$Gb:		'gProcessedSignal'

> class(dd.micro)
[1] "RGList"
attr(,"package")
[1] "limma"


ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background = TRUE)


> ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background = TRUE)
Error in if (min(dd.aux$Rb) < 0) { :
missing value where TRUE/FALSE needed

> ddTGS.rma = rmaMicroRna(dd.micro, normalize = TRUE, background = TRUE)
Error in if (min(dd.aux$Rb) < 0) { :
missing value where TRUE/FALSE needed



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