Question: Export expressionSet to ArrayExpress "processed data"
0
gravatar for Steffen Neumann
2.7 years ago by
Germany
Steffen Neumann30 wrote:

Hi,

ArrayExpress allows to submit raw and processed data. The latter is "a two-dimensional spreadsheet files in tab-delimited text (.txt) format" [2].

Question: has anyone a minimalistic snippet of R, exemplifying how to produce/export such preprocessed data, something similar to:

  library(simpleaffy)
  library(ath1121501.db)

  abatch <- read.affy(path=..., covdesc=...)
  eset <- rma(abatch)
  data <- exprs(eset)

  write.delim(data, file="mtab3305_eset.txt", formatoptions)

In particular, I'd be interested what are recommended formatoptions, such that gene annotation etc. will not break import into other software (quoting ? row/column names ?). Bonus points if this can be read directly back with package ArrayExpress [4] via ArrayExpress::procset(mtab3305, columnname).

Thanks in advance,
yours,
Steffen

[1] http://www.ebi.ac.uk/arrayexpress/
[2] https://www.ebi.ac.uk/fg/annotare/help/accepted_processed_ma_file_formats.html
[3] https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3305/
[4] https://bioconductor.org/packages/release/bioc/html/ArrayExpress.html

 

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Steffen Neumann30
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