Reading GSE Files using Readaffy Function.

Question

[12021560-040]

I have downloaded GSE file through R and unzip these files to extract CEL files. Now I want to read these cel files by using readAffy function for that purpose I am using commands 1. library(affy) # to load library 2. raw.data=ReadAffy(verbose=TRUE, filenames=cels, cdfname="Genechip") but this returns me an error mentioned below Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget, : object 'cels' not found what should I do know? Am I using correct commands?Please guide me.

Answer 1

[mastal511]

I can see two errors.

1. cdfname="Genechip". cdfname should be the name of the R cdf file for the specific type of Affymetrix array the data comes from. But you don't usually need to specify the name of the file, if you omit this parameter R should find the right cdf file automatically.

2. filenames=cels. You can omit the filenames parameter if all the files in your working directory are cel files, and you want ReadAffy to read all of them, otherwise you should supply a vector with the names of all the cel files you want it to read.

See the vignette for the Bioconductor affy package,

http://bioconductor.org/packages/release/bioc/vignettes/affy/inst/doc/affy.pdf

[12021560-040]

Reading cel files through readAffy I have given the command 1-library(affy) #this returns 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 objects are masked from ‘package:stats’: IQR, mad, 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, grep, grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, 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")' raw.data=ReadAffy(verbose=TRUE) #this returns 1 reading C:/Users/admin/Documents/cels.CEL ...instantiating an AffyBatch (intensity a 287296x18 matrix)...done. Reading in : C:/Users/admin/Documents/cels.CEL Reading in : C:/Users/admin/Documents/GSM533286.CEL Reading in : C:/Users/admin/Documents/GSM533287.CEL Reading in : C:/Users/admin/Documents/GSM533288.CEL Reading in : C:/Users/admin/Documents/GSM533289.CEL Reading in : C:/Users/admin/Documents/GSM533290.CEL Reading in : C:/Users/admin/Documents/GSM533291.CEL Reading in : C:/Users/admin/Documents/GSM533292.CEL Reading in : C:/Users/admin/Documents/GSM533293.CEL Reading in : C:/Users/admin/Documents/GSM533294.CEL Reading in : C:/Users/admin/Documents/GSM533295.CEL Reading in : C:/Users/admin/Documents/GSM533296.CEL Reading in : C:/Users/admin/Documents/GSM533297.CEL Reading in : C:/Users/admin/Documents/GSM533298.CEL Reading in : C:/Users/admin/Documents/GSM533299.CEL Reading in : C:/Users/admin/Documents/GSM533300.CEL Reading in : C:/Users/admin/Documents/GSM533301.CEL Reading in : C:/Users/admin/Documents/GSM533302.CEL 3-data.rma.norm=rma(raw.data) #this returns installing the source package ‘hu6800cdf’ trying URL 'https://bioconductor.org/packages/3.2/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz' Content type 'application/x-gzip' length 431388 bytes (421 KB) downloaded 421 KB * installing source package 'hu6800cdf' ... * R * data * preparing package for lazy loading Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hu6800cdf' Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hu6800cdf' * help * installing help indices * building package indices * testing if installed package can be loaded Warning: replacing previous import 'AnnotationDbi::head' by 'utils::head' when loading 'hu6800cdf' Warning: replacing previous import 'AnnotationDbi::tail' by 'utils::tail' when loading 'hu6800cdf' * DONE (hu6800cdf) The downloaded source packages are in ‘C:\Users\admin\AppData\Local\Temp\RtmpU1iKzP\downloaded_packages’ Background correcting Normalizing Calculating Expression Warning messages: 1: closing unused connection 3 (http://www.bioconductor.org/main.html) 2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hu6800cdf’ 3: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hu6800cdf’ Am I getting something relevant? Am I giving correct commands in correct orders? Please do help.

Answer 2

[mastal511]

If you go to the vignette I gave a link to above, on page 8 they work through an example with a dataset named Dilution, from the affydata package. If you work through their example code, it will give you an idea of how the functions in the affy package work, what kind of output to expect when they are running, and how to know when the code completes successfully.