Question: Reading cel files through readAffy
0
gravatar for 12021560-040
3.0 years ago by
12021560-04060
Pakistan
12021560-04060 wrote:

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.

readaffy .cell files R • 1.3k views
ADD COMMENTlink modified 3.0 years ago by geek_y9.3k • written 3.0 years ago by 12021560-04060
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