hi friends, i downloaded GSE67376_RAW and did like belowe that i got error but i do not know the reason...
> biocLite("affy")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.3), R version 3.2.1.
Installing package(s) ‘affy’
also installing the dependencies ‘BiocGenerics’, ‘Biobase’, ‘affyio’, ‘preprocessCore’, ‘zlibbioc’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/BiocGenerics_0.14.0.zip'
Content type 'application/zip' length 894569 bytes (873 KB)
downloaded 873 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/Biobase_2.28.0.zip'
Content type 'application/zip' length 4218443 bytes (4.0 MB)
downloaded 4.0 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/affyio_1.36.0.zip'
Content type 'application/zip' length 306444 bytes (299 KB)
downloaded 299 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/preprocessCore_1.30.0.zip'
Content type 'application/zip' length 414031 bytes (404 KB)
downloaded 404 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/zlibbioc_1.14.0.zip'
Content type 'application/zip' length 693703 bytes (677 KB)
downloaded 677 KB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/affy_1.46.1.zip'
Content type 'application/zip' length 2876604 bytes (2.7 MB)
downloaded 2.7 MB
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘affyio’ successfully unpacked and MD5 sums checked
package ‘preprocessCore’ successfully unpacked and MD5 sums checked
package ‘zlibbioc’ successfully unpacked and MD5 sums checked
package ‘affy’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mu\AppData\Local\Temp\RtmpSszekT\downloaded_packages
Old packages: 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'MASS',
'nlme', 'nnet', 'rpart', 'spatial', 'survival'
Update all/some/none? [a/s/n]: n
> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
rownames, sapply, setdiff, sort, table, tapply, union, unique,
unlist, unsplit
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
> affy.data = ReadAffy()
> eset.mas5 = mas5(affy.data)
background correction: mas
PM/MM correction : mas
expression values: mas
background correcting...also installing the dependencies ‘IRanges’, ‘GenomeInfoDb’, ‘DBI’, ‘RSQLite’, ‘S4Vectors’, ‘AnnotationDbi’
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/IRanges_2.2.5.zip'
Content type 'application/zip' length 3214870 bytes (3.1 MB)
downloaded 3.1 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/GenomeInfoDb_1.4.1.zip'
Content type 'application/zip' length 893594 bytes (872 KB)
downloaded 872 KB
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.2/DBI_0.3.1.zip'
Content type 'application/zip' length 158993 bytes (155 KB)
downloaded 155 KB
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.2/RSQLite_1.0.0.zip'
Content type 'application/zip' length 1214527 bytes (1.2 MB)
downloaded 1.2 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/S4Vectors_0.6.1.zip'
Content type 'application/zip' length 1628985 bytes (1.6 MB)
downloaded 1.6 MB
trying URL 'http://bioconductor.org/packages/3.1/bioc/bin/windows/contrib/3.2/AnnotationDbi_1.30.1.zip'
Content type 'application/zip' length 9453861 bytes (9.0 MB)
downloaded 9.0 MB
package ‘IRanges’ successfully unpacked and MD5 sums checked
package ‘GenomeInfoDb’ successfully unpacked and MD5 sums checked
package ‘DBI’ successfully unpacked and MD5 sums checked
package ‘RSQLite’ successfully unpacked and MD5 sums checked
package ‘S4Vectors’ successfully unpacked and MD5 sums checked
package ‘AnnotationDbi’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\mu\AppData\Local\Temp\RtmpSszekT\downloaded_packages
installing the source package ‘citruscdf’
trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/citruscdf_2.16.0.tar.gz'
Content type 'application/x-gzip' length 2424280 bytes (2.3 MB)
downloaded 2.3 MB
* installing *source* package 'citruscdf' ...
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (citruscdf)
The downloaded source packages are in
‘C:\Users\mu\AppData\Local\Temp\RtmpSszekT\downloaded_packages’
done.
30395 ids to be processed
| |
|####################|
> exprSet.nologs = exprs(eset.mas5)
> colnames(exprSet.nologs)
[1] "GSM1645665_120727-120222A_H_Citrus_.CEL"
[2] "GSM1645666_120727-120222B_D_Citrus_.CEL"
> exprSet = log(exprSet.nologs, 2)
> write.table(exprSet, file="Su_mas5_matrix.txt", quote=F, sep="\t")
>
> data.mas5calls = mas5calls(affy.data)
Getting probe level data...
Computing p-values
Error in FUN(X[[i]], ...) : NA/NaN/Inf in foreign function call (arg 2)
> write.table(data.mas5calls.calls, file="Su_mas5calls.txt", quote=F, sep="\t")
Error in is.data.frame(x) : object 'data.mas5calls.calls' not found
>
