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Karthik K N
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200
@karthik-k-n-5092
Last seen 10.3 years ago
Hello Marc,
I am trying to create an annotation package for Agilent 8x60K human
gene
expression array using SQLForge. I have a agilent_ID.txt file with
Agilent
Probe IDs in the first column and Entrez Gene IDs in the second
column. I
am using the following code:
>library("human.db0")
>agilent_IDs = system.file("extdata", "agilent_ID.txt",
package="human.db0")
>myMeta = c("DBSCHEMA"="HUMANCHIP_DB", "ORGANISM"="Homo sapiens",
"SPECIES"="Human", "MANUFACTURER"="Agilent", "CHIPNAME"="Human whole
genome
8x60k Array ", "MANUFACTURERURL"="http://www.chem.agilent.com")
>tmpout = tempdir()
>available.chipdbschemas()
>populateDB("HUMANCHIP_DB", affy = FALSE, prefix = "Agilent 8x60K",
fileName = agilent_IDs, metaDataSrc = myMeta, baseMapType = "eg",
outputDir
= tmpout)
>seed <- new("AnnDbPkgSeed", Package = "Agilent 8x60K.db", Version =
"1.0.0", PkgTemplate = "HUMANCHIP.DB", AnnObjPrefix = "Agilent 8x60K")
>makeAnnDbPkg(seed, file.path(tmpout, "Agilent 8x60K.sqlite"),
dest_dir =
tmpout)
simplifying probes table
dropping redundant data
Creating package in
C:\Users\1288\AppData\Local\Temp\Rtmp6JV7Qu/Agilent
8x60K.db
*Then, when I try to install the package using the code given below:*
>install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent
8x60K.db", repos=NULL, type="source")
*I am getting the error shown below:*
*
*
Installing package(s) into C:/Users/1288/Documents/R/win-
library/2.15
(as lib is unspecified)
* installing *source* package 'Agilent 8x60K.db' ...
Error : Invalid DESCRIPTION file
Malformed package name
See the information on DESCRIPTION files in section 'Creating R
packages' of the 'Writing R Extensions' manual.
ERROR: installing package DESCRIPTION failed for package 'Agilent
8x60K.db'
* removing 'C:/Users/kalash1288/Documents/R/win-library/2.15/Agilent
8x60K.db'
Warning messages:
1: running command 'C:/PROGRA~1/R/R-215~1.0/bin/x64/R CMD INSTALL -l
"C:/Users/1288/Documents/R/win-library/2.15"
"C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db"' had
status 1
2: In
install.packages("C:/Users/1288/AppData/Local/Temp/Rtmp6JV7Qu/Agilent
8x60K.db", :
installation of package
C:/Users/1288/AppData/Local/Temp/RTMP6J~1/Agilent 8x60K.db had non-
zero
exit status
Can you please help me solve this problem? Where am I making a
mistake?
I am also providing the session info below.
Thanks a lot for your help.
Regards,
Karthik
--------------------------------
*Session Info*
R version 2.15.0 (2012-03-30)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C
[5] LC_TIME=English_India.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RSQLite_0.11.1 DBI_0.2-5 AnnotationDbi_1.18.1
[4] Biobase_2.16.0 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] IRanges_1.14.4 limma_3.12.1 limmaGUI_1.32.0 stats4_2.15.0
[5] tcltk_2.15.0 tools_2.15.0
>
> ---------- Forwarded message ----------
> From: Marc Carlson <mcarlson@fhcrc.org>
> Date: Wed, Jun 20, 2012 at 12:28 AM
> Subject: Re: [BioC] Annotation Database for Agilent 8x60K Human Gene
> Expression Arrays
> To: bioconductor@r-project.org
>
>
> Hi Karthik,
>
> The 8x60 arrays have a different design ID so out of caution, I
would not
> recommend that you use that package for this. Even if all the IDs
from the
> other design id are present here (and that is a big if), you may
still in
> certain circumstances end up thinking that you tried to measure a
bunch of
> things that you did not try to measure. The design ID was put into
the
> name to try and avoid this confusion and to warn you about possible
> inconsistencies.
>
> Here is the page from Agilents website that gives the design IDs for
the
> platforms in question along with links to their eArray web
application that
> allows access to the files which they supply probe mappings for.
>
> http://www.genomics.agilent.**com/CollectionSubpage.aspx?**
> PageType=Product&SubPageType=**ProductData&PageID=1516<http: www.ge="" nomics.agilent.com="" collectionsubpage.aspx?pagetype="Product&SubPageType" =productdata&pageid="1516">
>
> From that eArray link you should be able to just download the file
(one
> for the 8x60 arrays) and then just follow the directions from the
SQLForge
> vignette from the AnnotationDbi package to make an annotation
package for
> the 8x60 arrays. It's pretty easy to make an annotation package.
The
> tricky part is usually getting the mapping information from the
> manufacturers, but it sounds like you have already done that part.
>
> Here is where you can find that SQLForge vignette:
>
> http://www.bioconductor.org/**packages/2.10/bioc/vignettes/**
> AnnotationDbi/inst/doc/**SQLForge.pdf<http: www.bioconductor.org="" pa="" ckages="" 2.10="" bioc="" vignettes="" annotationdbi="" inst="" doc="" sqlforge.pdf="">
>
>
> For more information about the Agi4x44PreProcess you should look at
the
> vignette for that package here:
>
> http://www.bioconductor.org/**packages/2.10/bioc/vignettes/**
> Agi4x44PreProcess/inst/doc/**Agi4x44PreProcess.pdf<http: www.biocon="" ductor.org="" packages="" 2.10="" bioc="" vignettes="" agi4x44preprocess="" inst="" doc="" agi="" 4x44preprocess.pdf="">
>
> The vignette certainly makes it seem like you can use this package
with
> other Agilent annotations, but you might want to ask Pedro about
exactly
> how accommodating his design is intended to be.
>
> Hope this helps,
>
>
> Marc
>
>
>
>
> On 06/18/2012 04:09 AM, Karthik K N wrote:
>
>> Dear Members (and especially Marc Carlson),
>>
>> I have few questions:
>>
>> 1. I was wondering whether HsAgilentDesign026652.db is the latest
updated
>> database for Agilent 8x60K human gene expression arrays or is there
any
>> other file? I have been told by Axel that HsAgilentDesign026652.db
cover
>> the oligos used by the Agilent 4x44Kv2 arrays, so I am not sure if
I can
>> use this for 8x60K arrays.
>>
>> 2. If I can indeed use HsAgilentDesign026652.db for 8x60K arrays,
is it
>> possible to use it as annotation file for Agi4x44PreProcess package
so
>> that
>> I can use the same codes from this package to analyze 8x60K arrays?
>>
>> 3. If I want to create an annotation file to be used in any of the
>> packages, what are the requirements (files, tools etc) for it? I
have an
>> annotation file in excel format given to me by my microarray
service
>> provider, so If I want to use that annotation file in
Agi4x44Preprocess
>> package (or any other package that requires this file) what should
I do?
>>
>> Thanks a lot in advance for all your suggestions!
>>
>> Cheers,
>>
>> Karthik
>>
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>>
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