Reading Affymetrix data from pd.hugene.2.0.st using affy
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kanacska ▴ 10
@kanacska-7375
Last seen 6.2 years ago
Hungary

Hi,

I'm working with this type of array(hugene 2.0) for the first time, i have CEL files for it and i used ReadAffy() but it didn't work. I've got this message: 

> raw <- ReadAffy()
Error: 

The affy package is not designed for this array type.
Please use either the oligo or xps package.

I've tried to download xps, it said: 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.0 (BiocInstaller 1.16.2), ?biocLite for help
> biocLite("xps")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'xps'

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

Warning message:
package ‘xps’ is not available (as a binary package for R version 3.1.3) 

What do i have to do so my CEL file is read in R so i can normalize it do limma with it. Or is there a way to convert my CEL file to CDF file???

Thank you for your answers.

Cheers,

Anna

affy pd.hugene.2.0.st hugene20 annotation microarray • 1.8k views
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cstrato ★ 3.9k
@cstrato-908
Last seen 3.2 years ago
Austria

Dear Anna,

Please supply your sessionInfo(), otherwise I don't know which system you are using.

To install xps you need to install ROOT first, see:

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

You can download 'root_v5.34.24' from: ftp://root.cern.ch/root/

If you use Windows you need to download ROOT from:

https://docs.google.com/file/d/0B0qZ3XBoK1ubVzl5MHBEaWxQdW8/edit

However, for Windows only a 32 bit version is supported.

 

Regards,

Christian

 

 

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kanacska ▴ 10
@kanacska-7375
Last seen 6.2 years ago
Hungary

Dea Christian, 

 

Tyank you for your quick answer!!

 

> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)

locale:
[1] LC_COLLATE=Hungarian_Hungary.1250  LC_CTYPE=Hungarian_Hungary.1250   
[3] LC_MONETARY=Hungarian_Hungary.1250 LC_NUMERIC=C                      
[5] LC_TIME=Hungarian_Hungary.1250    

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

other attached packages:
 [1] pd.hugene.2.0.st_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] pheatmap_1.0.2          limma_3.22.7            optparse_1.3.0         
[13] hgu133plus2cdf_2.15.0   affy_1.44.0             Biobase_2.26.0         
[16] BiocGenerics_0.12.1     BiocInstaller_1.16.2   

loaded via a namespace (and not attached):
 [1] affxparser_1.38.0     affyio_1.34.0         AnnotationDbi_1.28.2  bit_1.1-12           
 [5] codetools_0.2-11      colorspace_1.2-6      ff_2.2-13             foreach_1.4.2        
 [9] GenomeInfoDb_1.2.4    GenomicRanges_1.18.4  getopt_1.20.0         grid_3.1.3           
[13] gtable_0.1.2          iterators_1.0.7       munsell_0.4.2         plyr_1.8.1           
[17] preprocessCore_1.28.0 RColorBrewer_1.1-2    Rcpp_0.11.5           scales_0.2.4         
[21] splines_3.1.3         tools_3.1.3           zlibbioc_1.12.0      

Cheers,

Anna

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Entering edit mode
kanacska ▴ 10
@kanacska-7375
Last seen 6.2 years ago
Hungary

Eventually oligopackage worked, But i still have few questions.

 

celdir <- create celdir path
setwd(celdir)
setwd(celdir) #set working directory


# create sampleNames from the list of celFiles - substitute file names with sample names
raw<- list.celfiles('path of my cell files', full.names=TRUE)
filename2sample <- ('path of the txt')
fn2sp <- read.table(filename2sample, header=T)
sNames <- unlist(lapply(celFiles, convertFilename2Sample, tabledict=fn2sp)) # co

#I've found this for reading cell file

affyGeneFS <- read.celfiles(raw)
norm <- rma(affyGeneFS, target = "probeset")

Background correcting
Normalizing
Calculating Expression
Warning message:
'isIdCurrent' is deprecated.
Use 'dbIsValid' instead.
See help("Deprecated") 

What do i have to do if I get these message, or if i can continue working then it can stay like that???

expr<- exprs(norm)

AFTER THIS STEP CAN I USE limma as same as in affy u133 plus??

And in u133 there was a function for annotation:

library(hgu133plus2.db)

transcriptclusterid2symbol_many <- select(hgu133plus2.db,
                                          keys = keys(hgu133plus2.db),
                                          columns=c("PROBEID","ENTREZID","SYMBOL","MAP"),
                                          keytype="PROBEID")

Is there a same function in hugene 2.0??

Or is there a pipeline for hugene 2.0 analyses??

Cheers, 

Anna

 

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