[BioC] help

rakesh sharma [guest] guest at bioconductor.org
Tue Aug 14 11:30:46 CEST 2012

  i am new on R language and dealing with light-cycler qpcr data using HtqPCR package.everything goes all right till fold change.

when i use t-test then following error occured.

>  qDE.ttest <- ttestCtData(sr.norm[, 1:2], groups = files$Treatment[1:2], calibrator = "Control")
Error in t.test.default(x[, g1], x[, g2], alternative = alternative, paired = paired,  :
  data are essentially constant

when i select 4 samples then

qDE.ttest <- ttestCtData(sr.norm[, 1:4], groups = files$Treatment[1:4], calibrator = "Control")
Error in ttestCtData(sr.norm[, 1:4], groups = files$Treatment[1:4], calibrator = "Control") :
  Two factor levels required for 'groups'

my parent file look like this

File    Treatment
control.txt    Control
30min.txt    30min
2hr.txt    2hr
4hr.txt    4hr
8hr.txt    8hr
12hr.txt    12hr
16hr.txt    16hr
24hr.txt    24hr
48hr.txt    48hr

every sample have 26 features(13 replicate)
so how i perform t- test on these data.
please sir help me out.

thanking you

 -- output of sessionInfo(): 

R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] HTqPCR_1.10.0      limma_3.12.1       RColorBrewer_1.0-5 Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] affy_1.34.0           affyio_1.24.0         BiocInstaller_1.4.7   gdata_2.11.0          gplots_2.11.0        
 [6] gtools_2.7.0          preprocessCore_1.18.0 stats4_2.15.1         tools_2.15.1          zlibbioc_1.2.0     

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