Thanks Valerie,
Now I understand the readQualityScore. I ran your example code, the first few steps worked well till the report generation step. I got the same error as in my own example.

> report(res)
Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), width,  : 
  unable to start device JPEG
In addition: Warning message:
In jpeg(file.path(imgDir, jpegFile), ...) :
  no jpeg support in this version of R

It seems to me that I will have to ungrade to R 2.12. If I ungrade, the bioconductor I get will be the devel version using biocLite(), right?

Below is my current session info. Thanks again for the help!

> sessionInfo()
R version 2.11.1 (2010-05-31) 
x86_64-unknown-linux-gnu 

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

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

other attached packages:
 [1] CSAMA10_0.0.3          chipseq_0.4.1          GenomicFeatures_1.0.10
 [4] biomaRt_2.4.0          BSgenome_1.16.5        EatonEtAlChIPseq_0.0.1
 [7] rtracklayer_1.8.1      RCurl_1.4-3            bitops_1.0-4.1        
[10] ShortRead_1.6.2        Rsamtools_1.0.8        lattice_0.18-8        
[13] Biostrings_2.16.9      GenomicRanges_1.0.9    IRanges_1.6.17        

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 DBI_0.2-5     grid_2.11.1   hwriter_1.2   RSQLite_0.9-2
[6] tools_2.11.1  XML_3.1-1    




      
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