[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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