Dear Bioconductor List,

	I am new to RNASeq. I am running the script that comes
with easyRNAseq a command at a time to learn the program.
I got warning messages. I am wondering if they are indicative of
something being  wrong with my installation because I 
did not expect warnings in a tutorial script. Here is my
session,

###################################################################################
R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
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[R.app GUI 1.52 (6188) x86_64-apple-darwin9.8.0]

[History restored from /Users/friedman/.Rapp.history]

> getwd()
[1] "/Users/friedman"
> library("easyRNASeq")
Loading required package: parallel
Loading required package: genomeIntervals
Loading required package: intervals
Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map,
    mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor,
    see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: biomaRt
Loading required package: edgeR
Loading required package: limma
Loading required package: Biostrings
Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:intervals’:

    reduce


Attaching package: ‘Biostrings’

The following object(s) are masked from ‘package:intervals’:

    type

Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: DESeq
Loading required package: locfit
locfit 1.5-8 	 2012-04-25

Attaching package: ‘locfit’

The following object(s) are masked from ‘package:GenomicRanges’:

    left, right

Loading required package: Rsamtools
Loading required package: ShortRead
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Warning messages:
1: replacing previous import ‘coerce’ when loading ‘intervals’ 
2: replacing previous import ‘initialize’ when loading ‘intervals’
> library("RnaSeqTutorial")
> library(BSgenome.Dmelanogaster.UCSC.dm3)
> 
> library("easyRNASeq")
> library("RnaSeqTutorial")
> library(BSgenome.Dmelanogaster.UCSC.dm3)
> 
> count.table <- easyRNASeq(filesDirectory=system.file(
+                             "extdata",
+                             package="RnaSeqTutorial"),
+                           pattern="[A,C,T,G]{6}\\.bam$",
+                           format="bam",
+                           readLength=36L,
+                           organism="Dmelanogaster",
+                           chr.sizes=as.list(seqlengths(Dmelanogaster)),
+                           annotationMethod="rda",
+                           annotationFile=system.file(
+                             "data",
+                             "gAnnot.rda",
+                             package="RnaSeqTutorial"),
+                           count="exons"
+                           )
Checking arguments... 
Fetching annotations... 
Summarizing counts... 
Processing ACACTG.bam 
Processing ACTAGC.bam 
Processing ATGGCT.bam 
Processing TTGCGA.bam 
Preparing output 
There were 11 warnings (use warnings() to see them)
> 
> 
> warnings() 
Warning messages:
1: In easyRNASeq(filesDirectory = system.file("extdata",  ... :
  You enforce UCSC chromosome conventions, however the provided chromosome size list is not compliant. Correcting it.
2: In easyRNASeq(filesDirectory = system.file("extdata",  ... :
  There are 50573 features/exons defined in your annotation that overlap! This implies that some reads will be counted more than once! Is that really what you want?
3: In easyRNASeq(filesDirectory = system.file("extdata",  ... :
  You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it.
4: In fetchCoverage(obj, format = format, filename = file,  ... :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
5: In fetchCoverage(obj, format = format, filename = file,  ... :
  The read length stored in the object (probably provided as argument): 36
is not the same as the one: 30 determined from the file: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extdata/ACACTG.bam 
Updating it.
6: In fetchCoverage(obj, format = format, filename = file,  ... :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
7: In fetchCoverage(obj, format = format, filename = file,  ... :
  The read length stored in the object (probably provided as argument): 36
is not the same as the one: 30 determined from the file: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extdata/ACTAGC.bam 
Updating it.
8: In fetchCoverage(obj, format = format, filename = file,  ... :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
9: In fetchCoverage(obj, format = format, filename = file,  ... :
  The read length stored in the object (probably provided as argument): 36
is not the same as the one: 30 determined from the file: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extdata/ATGGCT.bam 
Updating it.
10: In fetchCoverage(obj, format = format, filename = file,  ... :
  You enforce UCSC chromosome conventions, however the provided alignments are not compliant. Correcting it.
11: In fetchCoverage(obj, format = format, filename = file,  ... :
  The read length stored in the object (probably provided as argument): 36
is not the same as the one: 30 determined from the file: /Library/Frameworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extdata/TTGCGA.bam 
Updating it.
> 
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

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

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

other attached packages:
 [1] BSgenome.Dmelanogaster.UCSC.dm3_1.3.17 RnaSeqTutorial_0.0.9                  
 [3] easyRNASeq_1.2.3                       ShortRead_1.14.4                      
 [5] latticeExtra_0.6-19                    RColorBrewer_1.0-5                    
 [7] lattice_0.20-6                         Rsamtools_1.8.5                       
 [9] DESeq_1.8.3                            locfit_1.5-8                          
[11] BSgenome_1.24.0                        GenomicRanges_1.8.7                   
[13] Biostrings_2.24.1                      IRanges_1.14.4                        
[15] edgeR_2.6.10                           limma_3.12.1                          
[17] biomaRt_2.12.0                         Biobase_2.16.0                        
[19] genomeIntervals_1.12.0                 BiocGenerics_0.2.0                    
[21] intervals_0.13.3                      

loaded via a namespace (and not attached):
 [1] annotate_1.34.1      AnnotationDbi_1.18.1 bitops_1.0-4.1       DBI_0.2-5            genefilter_1.38.0   
 [6] geneplotter_1.34.0   grid_2.15.1          hwriter_1.3          RCurl_1.91-1         RSQLite_0.11.1      
[11] splines_2.15.1       stats4_2.15.1        survival_2.36-14     XML_3.9-4            xtable_1.7-0        
[16] zlibbioc_1.2.0      
> 

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I would appreciate any suggestions.

Thanks and best wishes,
Rich
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman@cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

"School is an evil plot to suppress my individuality"

Rose Friedman, age15


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