Question

Brainarray CDF with oligopackage

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pbachali ▴ 50

@pbachali-9651

Last seen 4.8 years ago

Hi, I have a dataset from mogene20st platform. I am able to use the oligo package and read the celfiles and get the annotations. I am unable to use the brainarray CDF to read the celfiles. I realized that it's not added in pdInfobuilder. I referred to other posts where the cdf has been Pdinfobuilder. https://support.bioconductor.org/p/72378/

I followed the same steps and created z and seed. I am not able to install it. This is the error that R is throwing me.

> install.packages("pd.mogene21stmmense/", type="source",repos = NULL)
* installing *source* package ‘pd.mogene21stmmense’ ...
** R
** byte-compile and prepare package for lazy loading
Warning: package ‘Biostrings’ was built under R version 3.5.2
Error in eval(exprs[i], envir) : Unable to locate DB file
Error : unable to load R code in package ‘pd.mogene21stmmense’
ERROR: lazy loading failed for package ‘pd.mogene21stmmense’
* removing ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pd.mogene21stmmense’
Warning in install.packages :
  installation of package ‘pd.mogene21stmmense/’ had non-zero exit status

Here is my code.

library(pdInfoBuilder)
library(ff)
library(doMC)
registerDoMC(10)
download.file("http://mbni.org/customcdf/19.0.0/ense.download/mogene21st_Mm_ENSE_19.0.0.zip","tmp.zip")
unzip("tmp.zip")
dir()
z <- cdf2table("mogene21st_Mm_ENSE.cdf")
seed <- new("GenericPDInfoPkgSeed", table=z, author = "me", email = "prathyusha.bachali@ampelbiosolutions.com", species = "Mus musculus", pkgName = "pd.mogene21stmmense")
makePdInfoPackage(seed)
install.packages("pd.mogene21stmmense/", type="source",repos = NULL)

Thanks in advance

Brainarray CDF oligo • 1.2k views

ADD COMMENT • link updated 5.5 years ago by James W. MacDonald 67k • written 5.5 years ago by pbachali ▴ 50

score 0 · Answer 1 · 2019-05-09

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 12 hours ago

United States

MBNI now builds pdInfoPackages that you can use directly.

> install.packages("http://mbni.org/customcdf/23.0.0/ense.download/pd.mogene21st.mm.ense_23.0.0.tar.gz", repos = NULL, type = "source")
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/3.5'
(as 'lib' is unspecified)
trying URL 'http://mbni.org/customcdf/23.0.0/ense.download/pd.mogene21st.mm.ense_23.0.0.tar.gz'
Content type 'application/x-gzip' length 11763911 bytes (11.2 MB)
downloaded 11.2 MB

* installing *source* package 'pd.mogene21st.mm.ense' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'pd.mogene21st.mm.ense'
    finding HTML links ... done
    pkg                                     html  
    probeSequences                          html  
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (pd.mogene21st.mm.ense)
In R CMD INSTALL

ADD COMMENT • link 5.5 years ago James W. MacDonald 67k

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Thanks a lot. I really appreciate it. I am trying to get the gene symbols, entrezgene for the features from the pd.mogene21st.mm.ense. I am trying to use biomrt but not able to get any results. library(annotate) ID <- featureNames(esetba) Symbol <- getSYMBOL(ID,"mogene21stmmentrezg.db") fData(esetba) <- data.frame(Symbol=Symbol)

But this approach gave me 0 gene symbols.

ADD REPLY • link 5.5 years ago pbachali ▴ 50

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Your first post no longer makes sense to me. Do you want the mapping to be based on Ensembl (hence ense in the name) or NCBI (hence entrezg in the name)? If you want NCBI IDs, then you need to install from 'http://mbni.org/customcdf/23.0.0/entrezg.download/pd.mogene21st.mm.entrezg_23.0.0.tar.gz'.

I also pointed you to the wrong thing (probably). The mapping I used was 'ense' which is for Ensembl exon mappings, whereas you probably want the gene level mappings.

AND, the featureNames for any of the MBNI data are simply the underlying ID with an '_at' pasted on the end. So for example, the IDs for the ense package I installed yesterday are


> con <- db(pd.mogene21st.mm.ense)
> dbListTables(con)
[1] "featureSet1" "mps1pm"      "pmfeature"   "table_info" 
> DBI::dbGetQuery(con, "select * from featureSet1 limit 20;")
   fsetid            man_fsetid       type direction
1       1 ENSMUSE00000097912_at expression antisense
2       2 ENSMUSE00000097957_at expression antisense
3       3 ENSMUSE00000097958_at expression antisense
4       4 ENSMUSE00000097959_at expression antisense
5       5 ENSMUSE00000097960_at expression antisense
6       6 ENSMUSE00000097961_at expression antisense
7       7 ENSMUSE00000097962_at expression antisense
8       8 ENSMUSE00000097964_at expression antisense
9       9 ENSMUSE00000097969_at expression antisense
10     10 ENSMUSE00000097971_at expression antisense
11     11 ENSMUSE00000097973_at expression antisense
12     12 ENSMUSE00000097977_at expression antisense
13     13 ENSMUSE00000097978_at expression antisense
14     14 ENSMUSE00000098001_at expression antisense
15     15 ENSMUSE00000098014_at expression antisense
16     16 ENSMUSE00000098055_at expression antisense
17     17 ENSMUSE00000098057_at expression antisense
18     18 ENSMUSE00000098058_at expression antisense
19     19 ENSMUSE00000098063_at expression antisense
20     20 ENSMUSE00000098065_at expression antisense

Where the manfsetid column has the probeset (or featureName) identifiers. There are annotation packages for the NCBI remapped arrays (e.g., http://mbni.org/customcdf/23.0.0/entrezg.download/mogene21stmmentrezg.db23.0.0.tar.gz), but those are sort of superfluous, as you can just as easily use the org.Hs.eg.db package after stripping off the '_at' from the probeset IDs.

Also getSymbol is old tech. You should be using either select or mapIds. And if you do use the annotation packages from MBNI, you can also use annotateEset from my affycoretools package to do the annotation.

ADD REPLY • link 5.5 years ago James W. MacDonald 67k