error in mas5

Question

[zizigolu]

Hi friends, I downloaded GSE67376_RAW and did like below 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

[poisonAlien]

Mas5calls uses both perfect match and mismatch probes to make present or absent calls. Most of the older chips (e.g; hgu133plus2) have mismatch probes but newer arrays like exon/st arrays lack mismatch probes, in which case mas5calls doesn't work. Make sure the chip you're using has mismatch probes for mas5calls to run. Even though it appears that the chip your using, has MM probes, make sure once from affymetrix website.

[zizigolu]

Yes I think so because I took R script from a tutorial in 2007

Answer 1

[PoGibas]

affy.data = ReadAffy()

It seems that affy.data is empty as you didn't read in any CEL files. ReadAffy command - "Read CEL files into an Affybatch". You have to specify files that you want to read in:

# Example
daffy <- ReadAffy("daffyFiles")

Also, this code from the github (processAffyData.R) by Obi Griffith might help you.

[zizigolu]

Thank you for your answer