gcrma problem with make.cdf.package
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0
Entering edit mode
Osvaldo ▴ 30
@osvaldo-6150
Last seen 17 months ago
Spain

Hi there !

I am posting this question because I am facing some problems with the gcrma package

The fact is that I must analyse GSE1133 microarrays (https://www.ncbi.nlm.nih.gov/gds?term=GSE1133 ), more specifically the subset of GPL1074 samples (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1074 ).

I have already downloaded all the GSE1133 files, as follows:

gset <- getGEO("GSE1133", GSEMatrix=TRUE, AnnotGPL=TRUE, destdir = WD, getGPL = TRUE)
filePaths = getGEOSuppFiles("GSE1133", baseDir= WD, makeDirectory = T, fetch_files = T)

Now, in order to go for the gcrma normalization, I did the following:

library(affyio)
f <- list.files(pattern = "CEL.gz")
table(sapply(f, function(x) read.celfile.header(x)$cdfName))
ff <- split(f, sapply(f, function(x) read.celfile.header(x)$cdfName))

Here comes the section where I am facing problems. I have tried two different approaches:

(Approach 1)

CDF=make.cdf.env(filename = "GPL1074.CDF.gz", cdf.path = WD, compress = TRUE, return.env.only = T, verbose = TRUE)
Reading CDF file.
Creating CDF environment
Wait for about 226 dots....................................................................................................................................................................................................
ab <- ReadAffy(filenames=ff$gnGNF1Ba, celfile.path=WD, cdfname = "CDF")
eset <- gcrma(ab)
Adjusting for optical effect..............................................................................................................................................................Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment cdfcdf was not found in the Bioconductor repository."
[1] "Checking to see if your internet connection works..."
[1] "Environment cdfprobe was not found in the Bioconductor repository."
Error in get(probepackagename) : object 'cdfprobe' not found

(Approach 2)

make.cdf.package("GPL1074.CDF",packagename="gngnf1bacdf", species = "Homo_sapiens")
(next, from the linux shell: R CMD INSTALL gngnf1bacdf)
once back in R:
library("gngnf1bacdf")
ab <- ReadAffy(filenames=ff$gnGNF1Ba, celfile.path=WD)
eset <- gcrma(ab)
Adjusting for optical effect..............................................................................................................................................................Done.
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Environment gngnf1baprobe was not found in the Bioconductor repository."
Error in get(probepackagename) : object 'gngnf1baprobe' not found

Do you have any clue about the source of the error?
Thank you very much in advance. I would really appreciate your help.

osvaldo.

PD: my R session info (just in case)

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=C.UTF-8           LC_NUMERIC=C            
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=C.UTF-8        
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=C.UTF-8      
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C      

attached base packages:<br />
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] gngnf1bacdf_1.60.0  gpl1074cdf_1.60.0   devtools_2.3.0     
 [4] usethis_1.6.1       makecdfenv_1.60.0   gcrma_2.56.0       
 [7] affy_1.62.0         Biobase_2.44.0      BiocGenerics_0.30.0
[10] affyio_1.54.0      <br />

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6          compiler_3.6.2        BiocManager_1.30.10  
 [4] XVector_0.24.0        prettyunits_1.1.1     remotes_2.1.1        
 [7] tools_3.6.2           zlibbioc_1.30.0       bit_1.1-15.2         
[10] testthat_2.3.2        digest_0.6.25         pkgbuild_1.0.7       
[13] pkgload_1.0.2         RSQLite_2.2.0         memoise_1.1.0       
[16] preprocessCore_1.46.0 rlang_0.4.5           DBI_1.1.0            
[19] cli_2.0.2             withr_2.2.0           vctrs_0.2.4          
[22] Biostrings_2.52.0     desc_1.2.0            fs_1.4.1             
[25] S4Vectors_0.22.1      IRanges_2.18.3        bit64_0.9-7          
[28] stats4_3.6.2          rprojroot_1.3-2       glue_1.4.0           
[31] R6_2.4.1              processx_3.4.2        AnnotationDbi_1.46.1 
[34] fansi_0.4.1           sessioninfo_1.1.1     blob_1.2.1           
[37] callr_3.4.3           magrittr_1.5          backports_1.1.6      
[40] ps_1.3.2              ellipsis_0.3.0        splines_3.6.2        
[43] assertthat_0.2.1      crayon_1.3.4
gcrma make.cdf.package affy • 246 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

To use gcrma you also need a probe package that can be used to determine the GC content of the probes. You can get the probe file here, which you will note is a supplemental file for GPL1073.

The probe file that was submitted has an extra column that we have to deal with first, so since you are on linux this is trivial. At a terminal

wget ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL1nnn/GPL1073/suppl/GPL1073%2Etab%2Egz
gzip -d GPL1073.tab.gz
cut -f 1,3-7 GPL1073.tab > gngnf1ba_probe_tab

And now in R

> makeProbePackage("gngnf1ba", maintainer = "me <me@mine.org>", version = "0.0.1", species = "Mus musculus", outdir = ".", check = FALSE, build = FALSE)
Importing the data.
Creating package in ./gngnf1baprobe 
Writing the data.
[1] "gngnf1baprobe"
> install.packages("gngnf1baprobe", repos = NULL, type = "source")  ## you don't need the type argument!
Installing package into 'C:/Users/jmacdon/AppData/Roaming/R/win-library/4.0'
(as 'lib' is unspecified)
* installing *source* package 'gngnf1baprobe' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gngnf1baprobe'
    finding HTML links ... done
    gngnf1baprobe                           html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (gngnf1baprobe)
> library(gngnf1baprobe)
>

I am doing this on Windows, so I need the 'type' argument. You won't need that.

ADD COMMENT
1
Entering edit mode

Hi James,

The way you have proposed has worked very well !!

Thank you very much !!

Best,

osvaldo

ADD REPLY
0
Entering edit mode

Hi James,

The way you have proposed has worked very well !!

Thank you very much !!

Best,

osvaldo

ADD REPLY
0
Entering edit mode

Hi James,

The way you have proposed has worked very well !!

Thank you very much !!

Best,
osvaldo

ADD REPLY

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