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Richard Friedman
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@richard-friedman-513
Last seen 10.2 years ago
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,
######################################################################
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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/Fram
eworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extd
ata/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/Fram
eworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extd
ata/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/Fram
eworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extd
ata/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/Fram
eworks/R.framework/Versions/2.15/Resources/library/RnaSeqTutorial/extd
ata/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
>
######################################################################
#############
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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