AGI code in gcrma normalization output
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Angel ▴ 40
@angel-7981
Last seen 4.5 years ago
Berlin

hi,

i am using RobiNA to perform gcrma normalization on my arabidopsis thaliana CEL files. without using my ATH1121501_At_TAIRG.cdf file, the output is with Affymetrix ATH1 Genome Array  IDs like 267636_at but i need the output with TAIR locus ID like AT3G34250 but when using my ATH1121501_At_TAIRG.cdf file, i get this error

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

Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘limma’

The following object is masked from ‘package:BiocGenerics’:

plotMA

Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Computing affinities[1] "Checking to see if your internet connection works..."
[1] "Checking to see if your internet connection works..."
Calls: gcrma -> bg.adjust.gcrma -> compute.affinities -> get
Execution halted

i installed all of mentioned package. how i can have a gcrma normalized output with

TAIR locus ID like AT3G34250 please???

gcrma software error annotation • 954 views
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When providing information to help people diagnose your problem, the more important thing to show is your code! What you have provided is almost everything but the part that would actually be useful. In addition, this isn't really the site you should be consulting. Although RobiNA appears to use Bioconductor tools, it is wrapping those tools in some Java code that seems to be mucking things up. For instance, the AffyBatch apparently has its annotation slot changed to be 'importcdf', which is not the name of any array. Perhaps you need to already install something?

Anyway, if you want to use Bioconductor tools directly, then we are more than happy to help you get going. But if you want to use RobiNA, then you need to ask them what the problem is.

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thank you,

excuse me, i have another question, i was going to do vsn normalization on my arrays but i don't know how to write the result as a text file..i did like below

> setwd("E:/Affy data")

> library(affy)

> library(vsn)

> celFiles <- list.celfiles()
> affyraw.vsn2=vsn2(affyraw)
vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit.

but hereafter i don't know how to save the normalized file in a txt file because when i wrote like below i got these errors

> write.table(affyraw.vsn2, file = "arrayvsn.txt", dec = ".", sep = "\t", quote = FALSE)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
cannot coerce class "structure("vsn", package = "vsn")" to a data.frame

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Entering edit mode
@james-w-macdonald-5106
Last seen 18 hours ago
United States

You probably don't want to write to a text file. If you are going to use Bioconductor to analyze your data, then you should realize that most of the packages are intended to be used as part of a pipeline where you go from raw data to analyzed results, without ever writing things out to disk. At the end you might generate an HTML table or something, but there is almost never a good reason to write things out to text files (because then you just have to read back in again).

If you are using Affy data, then your best bet is probably to use vsnrma() instead of vsn2() anyway. That returns an ExpressionSet, which you can then analyze using something like limma.

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thank you very much