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Suyog Pol
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40
@suyog-pol-3909
Last seen 10.2 years ago
Hi
I have built an annotation package with the help of guidlines set in
the
vignette/document
"SQLforge by Marc Carlson et al." I am having problem installing it.
The following code was used for building the package:-
if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
mart<-useDataset("hsapiens_
gene_ensembl",mart)
ensemble.illumina <-
getBM(attributes=c("illumina_humanwg_6_v3","entrezgene"),filters="illu
mina_humanwg_6_v3",
values=illumina.humanv3.probeset, mart=mart,na.value = NA)
}
##ensemble.Illumina was written into a file and modified to satisfy
the
requisites of the input vector
##required for the function makeDBPackage. The following code was
used for
making the final
##package:-
> tmpout <- "Y:/path/to/annotation/package"
> library("human.db0")
Loading required package: AnnotationDbi
Loading .......
> library("AnnotationDbi")
> makeDBPackage("HUMANCHIP_DB",
+ affy=FALSE,
+ prefix="illuminaHumanv3_ensemble_beta",
+ fileName=filename,
+ baseMapType="eg",
+ outputDir = tmpout,
+ version="1.0.0",
+ manufacturer = "Illumina",
+ chipName = "HT-12",
+ manufacturerUrl = "http://www.illumina.com")
Loading required package: RSQLite
Loading required package: DBI
baseMapType is eg
Prepending Metadata
Creating Genes table
Appending Probes
Found 0 Probe Accessions
Appending Gene Info
Found 24758 Gene Names
Found 24758 Gene Symbols
Appending Chromosomes
Appending Cytogenetic Locations
Appending Omim
Appending RefSeq
Appending Pubmed
Appending Unigene
Appending ChrLengths
Appending 3 GO tables
Appending 3 GO ALL tables
Appending KEGG
Appending EC
Appending Chromosome Locations
Appending Pfam
Appending Prosite
Appending Alias
Appending Ensembl
Appending Uniprot
Appending Metadata
simplifying probes table
dropping redundant data
Creating package in
Y:/path/to/annotation/package/illuminaHumanv3_ensemble_beta.db
#To install the above package : -
>
install.packages("Y:/path/to/annotation/package/illuminaHumanv3_ensemb
le_beta.db",
+ repos = NULL)
*Warning in install.packages("Y:/Genomics/ArrayData/Jan 2010 -
CD140aO4
sorts/annotation/anno2/illuminaHumanv3_ensemble_beta.db", :
argument 'lib' is missing: using
'C:\Users\suyogpol\Documents/R/win-library/2.10'
Error in gzfile(file, "r") : cannot open the connection
In addition: Warning messages:
1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip
file
2: In gzfile(file, "r") :
cannot open compressed file
'illuminaHumanv3_ensemble_beta.db/DESCRIPTION', probable reason 'No
such
file or directory*
# I assumed that install.packages by default attempts to unzip the
requested
package file
#To fix this I zipped the package directory and re used the
install.packages
function:-
>setwd("Y:/path/to/annotation/package" )
> install.packages("illuminaHumanv3_ensemble_beta.db",
+ repos = NULL)
*Warning in install.packages("illuminaHumanv3_ensemble_beta.db", repos
=
NULL) :
argument 'lib' is missing: using
'C:\Default/location/of/library/R/win-library/2.10'
*
##I checked in my default library directory and a new folder for the
package
had been made
#But when I attempted to load the package using the library command :-
>library("illuminaHumanv3_ensemble_beta.db")
*Error in library("illuminaHumanv3_ensemble_beta.db") :
'illuminaHumanv3_ensemble_beta.db' is not a valid installed package
*
##I repeated the process using the lengthier method described in same
guide
#manual. This approach landed me in the same situation as the above.
Can someone help me to know if there is a mistake in my approach used
for
making or installing the annotation package.
Thanks in advance
Suyog P
> sessionInfo()
R version 2.10.1 (2009-12-14)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_0.8-1 DBI_0.2-5 human.db0_2.3.6
[4] AnnotationDbi_1.8.1 Biobase_2.6.1
loaded via a namespace (and not attached):
[1] tools_2.10.1
--
Masters Student
Department of Chemical and Biological Eng,
University at Buffalo,
Buffalo, NY .
Ph: 801 814 3893
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