Important r packages not available for R version 3.1.1
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svlachavas ▴ 780
@svlachavas-7225
Last seen 6 days ago
Germany/Heidelberg/German Cancer Resear…

Dear Bioconductor community,

i tried to install some r packages for exon array preprossesing and analysis. But especially in the package "exonmap", which i found from literature that is the simplest way of importing exon array data : Warning message:
package ‘exonmap’ is not available (for R version 3.1.1) .

Is there some other package(packages) for importing exon array data in R?

exonmap exon array analysis bioconductor • 4.4k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
United States

xps also requires that you have ROOT installed, which is described in the README:

http://bioconductor.org/packages/release/bioc/readmes/xps/README

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@steve-lianoglou-2771
Last seen 2 days ago
Denali

If you go to the software page and search for "exon", you will find that by their description, at least these two packages might be useful:

I believe people often use xps, but I've never really analyzed an exon array myself.

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Thank you- i also searched extensively for other packages, but unfortunately xps is also not available in my R version. Regarding puma, i didnt noticed that it can also read and impute exon data

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The xps package is available for your version of R. You can also use the oligo package. Also note that exonmap has been superceeded by the annmap package.
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Dear Mr MacDonald,

when i tried biocLite(c("xps")), it shows the message:

Warning message:
package ‘xps’ is not available (for R version 3.1.1) 

Also, when i tried the "annmap" package installation:

package ‘annmap’ is available as a source package but not as a binary

Warning message:
package ‘annmap’ is not available (for R version 3.1.1) 

Is it possible to install annmap with a different procedure ?

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You need to provide the full output of the biocLite() command so we can see where the error is. Also you need to give us the output of the sessionInfo() command so we can see  details about your setup. xps is not available for 64-bit R on Windows,  so you could try switching to 32-bit R if you are on Windows (I'll see if this restriction can be removed in the next version).

 

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svlachavas ▴ 780
@svlachavas-7225
Last seen 6 days ago
Germany/Heidelberg/German Cancer Resear…

biocLite(c("xps"))
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.1), R version 3.1.1.
Installing package(s) 'xps'

   package ‘xps’ is available as a source package but not as a binary

Warning message:
package ‘xps’ is not available (for R version 3.1.1)

 

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Greek_Greece.1253  LC_CTYPE=Greek_Greece.1253   
[3] LC_MONETARY=Greek_Greece.1253 LC_NUMERIC=C                 
[5] LC_TIME=Greek_Greece.1253    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] hgu133aprobe_2.15.0  AnnotationDbi_1.28.1 GenomeInfoDb_1.2.4   hgu133acdf_2.15.0   
 [5] puma_3.8.0           oligo_1.30.0         Biostrings_2.34.1    XVector_0.6.0       
 [9] IRanges_2.0.1        S4Vectors_0.4.0      oligoClasses_1.28.0  mclust_4.4          
[13] BiocInstaller_1.16.1 simpleaffy_2.42.0    gcrma_2.38.0         genefilter_1.48.1   
[17] affy_1.44.0          Biobase_2.26.0       BiocGenerics_0.12.1 

loaded via a namespace (and not attached):
 [1] affxparser_1.38.0     affyio_1.34.0         affyPLM_1.42.0       
 [4] annotate_1.44.0       bit_1.1-12            codetools_0.2-10     
 [7] DBI_0.3.1             ff_2.2-13             foreach_1.4.2        
[10] GenomicRanges_1.18.4  iterators_1.0.7       preprocessCore_1.28.0
[13] RSQLite_1.0.0         splines_3.1.1         survival_2.38-1      
[16] tools_3.1.1           XML_3.98-1.1          xtable_1.7-4         
[19] zlibbioc_1.12.0

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As I guessed, you are using 64-bit windows. Try starting R with the following command line:

R --arch i386

And then try to install xps. You'll need to invoke R that way every time you want to use xps. If you use R though a GUI you'll need to be sure you are starting the GUI in 32-bit mode as well. 

 

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i run R through Rstudio. So can i use the above code? Or can i change to 32-bit the R-studio ? Moreover, is it possible that also the other packages that i mentioned didnt worked because of the 64-bit windows? Please excuse me for these questions, but im fresh in R without any prior programming experience

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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 8 months ago
United States

This link should tell you how to have RStudio start the 32-bit version every time. Note that you need to restart RStudio after making this change:

https://support.rstudio.com/hc/en-us/articles/200486138-Using-Different-Versions-of-R

 

Dan

 

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Ok thank you again,  i have found also the above link. One last question(please excuse me again)about the change of R to 32bit: i have to reinstall all my packages or loose any other information ?

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No, you should not have to reinstall your packages.

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ok it seems that root is a bit tricky(for me i suppose without very good background) but i suppose i will find it. Moreover, in global options of Rstudio i changed from 64bit to 32bit, but again  some packages i mentioned above, they could not again be installed--i guess that maybe for this version of R they are not compatible

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Since you are using Windows you need to install a special version of ROOT, which is compiled with MinGW. However, this version is 32 bit only. 
Currently you can download this ROOT version from:
https://docs.google.com/file/d/0B0qZ3XBoK1ubVzl5MHBEaWxQdW8/edit

Please read the README file how to install ROOT and xps for Windows.

 

 

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i read it-but it says for windows i have to contact the author for sending a special file named 'root-mingw-O2.7z'

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Or you could just use the oligo package, which does work on Win64, and is simple to install.

> biocLite("oligo")

## use GEO dataset as example

> getGEOSuppFiles("GSE58038")
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58038/suppl/
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58038/suppl//GSE58038_RAW.tar'
using Synchronous WinInet calls
opened URL
downloaded 245.1 Mb

trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58038/suppl//filelist.txt'
using Synchronous WinInet calls
opened URL
downloaded 1047 bytes

> setwd("GSE58038/")
> untar("GSE58038_RAW.tar")
> library(oligo)

> dat <- read.celfiles(dir(".","CEL.gz"))

Platform design info loaded.
Reading in : GSM1399774_MY_FD2_DMSO_1_.CEL.gz
Reading in : GSM1399775_MY_FD2_DMSO_2_.CEL.gz
Reading in : GSM1399776_MY_FD2_DMSO_3_.CEL.gz
Reading in : GSM1399777_MY_FD2_2.0_1_.CEL.gz
Reading in : GSM1399778_MY_FD2_2.0_2_.CEL.gz
Reading in : GSM1399779_MY_FD2_2.0_3_.CEL.gz
> eset.core  <- rma(dat, target = "core")
Background correcting
Normalizing
Calculating Expression
Warning message:
'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")

> eset.probeset <- rma(dat, target = "probeset")
Background correcting
Normalizing
Calculating Expression
Warning message:
'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated")

> dat
ExonFeatureSet (storageMode: lockedEnvironment)
assayData: 6553600 features, 6 samples
  element names: exprs
protocolData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.huex.1.0.st.v2

> eset.core
ExpressionSet (storageMode: lockedEnvironment)
assayData: 22011 features, 6 samples
  element names: exprs
protocolData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.huex.1.0.st.v2

> eset.probeset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 1411399 features, 6 samples
  element names: exprs
protocolData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: exprs dates
  varMetadata: labelDescription channel
phenoData
  rowNames: GSM1399774_MY_FD2_DMSO_1_.CEL.gz GSM1399775_MY_FD2_DMSO_2_.CEL.gz
    ... GSM1399779_MY_FD2_2.0_3_.CEL.gz (6 total)
  varLabels: index
  varMetadata: labelDescription channel
featureData: none
experimentData: use 'experimentData(object)'
Annotation: pd.huex.1.0.st.v2 
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods 
[9] base     

other attached packages:
[1] pd.huex.1.0.st.v2_3.10.0 RSQLite_1.0.0            DBI_0.3.1              
[4] oligo_1.30.0             Biostrings_2.34.1        XVector_0.6.0          
[7] IRanges_2.0.1            S4Vectors_0.4.0          oligoClasses_1.28.0    
[10] GEOquery_2.32.0          Biobase_2.26.0           BiocGenerics_0.12.1    
[13] BiocInstaller_1.16.1    

loaded via a namespace (and not attached):
[1] affxparser_1.38.0     affyio_1.34.0         bit_1.1-12          
[4] bitops_1.0-6          codetools_0.2-8       ff_2.2-13           
[7] foreach_1.4.2         GenomeInfoDb_1.2.4    GenomicRanges_1.18.4
[10] iterators_1.0.7       preprocessCore_1.28.0 RCurl_1.95-4.5      
[13] splines_3.1.1         tools_3.1.1           XML_3.98-1.1        
[16] zlibbioc_1.12.0     
 
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Dear Mr. MacDonald, i would like to ask another important question regarding the above normalization, in terms of target="core" and target="probeset" . Which is more appropriate for my analysis to keep as far as i have exon array data? or it depends on my data? 

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thank you again for your references, i have also downloaded them. My main question need to be excluded from the experiment (which was a "polyA mRNA separation") is to identify which are the genes cleaved by the enzyme, IRE1, and on what exons---so, I believe  summarization in both levels might be essential.

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svlachavas ▴ 780
@svlachavas-7225
Last seen 6 days ago
Germany/Heidelberg/German Cancer Resear…

Thank you Mr  MacDonald for this valuable alternative implementation. My other rationale for trying to use xps from the begining, is that except for the exon dataset, i wanted to check if i can perform detection calls also in a PM-only dataset. On the other hand, from the oligo vignette i also noticed paCalls which also performs present/absent calls--thus i suppose i could try it for both the exon and the PM-only array.

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