Question: Human gene2.0ST analysis using R
0
gravatar for ttsutsui1028
2.6 years ago by
ttsutsui102820
ttsutsui102820 wrote:

Dear all,

I'm trying to process CEL file from Human gene2.0 ST array to make expression matrix file. While I tried to normalize signal using mas5 in affy package, I got following error message.

hoge<- read.celfiles(c("si cont.CEL", "si TREAT.CEL")) eset<- mas5(hoge) background correction: mas PM/MM correction : mas expression values: mas error in background correcting... (function (classes, fdef, mtable): unable to find an inherited method for function ‘bg.correct’ for signature ‘"GeneFeatureSet", "character"’

My condition is following.

sessionInfo() R version 3.2.3 (2015-12-10) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.11.6 (El Capitan)

locale: [1] ja_JP.UTF-8/ja_JP.UTF-8/ja_JP.UTF-8/C/ja_JP.UTF-8/ja_JP.UTF-8

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

other attached packages: [1] affy_1.48.0 pd.hugene.2.0.st_3.14.1 oligo_1.34.2 Biobase_2.30.0 oligoClasses_1.32.0
[6] RSQLite_1.0.0 DBI_0.5-1 Biostrings_2.38.4 XVector_0.10.0 IRanges_2.4.8
[11] S4Vectors_0.8.11 BiocGenerics_0.16.1

loaded via a namespace (and not attached): [1] affxparser_1.42.0 GenomicRanges_1.22.4 splines_3.2.3 zlibbioc_1.16.0
[5] bit_1.1-12 foreach_1.4.3 GenomeInfoDb_1.6.3 tools_3.2.3
[9] SummarizedExperiment_1.0.2 ff_2.2-13 iterators_1.0.8 preprocessCore_1.32.0
[13] affyio_1.40.0 codetools_0.2-14 BiocInstaller_1.20.3

Could someone advise me? Best, Taiki

microarray R software error • 999 views
ADD COMMENTlink modified 2.6 years ago by Charles Warden6.6k • written 2.6 years ago by ttsutsui102820
1
gravatar for Charles Warden
2.6 years ago by
Charles Warden6.6k
Duarte, CA
Charles Warden6.6k wrote:

You might want to review this post:

Difference Between Mas5 And Rma Normalisation. Which Is More Appropriate When?

If you have HuGene arrays, you should use RMA (or GCRMA) normalization, since you don't have mismatch probes (although you have other types of control probes). You can either do this using the oligo package or affy power tools:

https://bioconductor.org/packages/release/bioc/html/oligo.html

http://www.affymetrix.com/estore/support/developer/powertools/changelog/apt-probeset-summarize.html.affx;jsessionid=930E8EFDA117BB0FC7AAF354D35B40BA

ADD COMMENTlink written 2.6 years ago by Charles Warden6.6k
1

Thank you Charles.

rma command works fine in the oligo package in my hand. However, It looks reasonable to use affy power tools rather than using R. I will try affy power tool, too. Thanks again, Taiki

ADD REPLYlink written 2.6 years ago by ttsutsui102820
0
gravatar for ssv.bio
2.6 years ago by
ssv.bio180
ssv.bio180 wrote:

I am not sure about the error. However, try using oligo package (seems to be working for affy exon arrays). It supports mas5 background correction.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by ssv.bio180
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