Question: How can I loading and normalising the data for (HuGene-1_0-st-v1) microarray Data In Bioconductor
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gravatar for AAhmed
2.9 years ago by
AAhmed20
AAhmed20 wrote:

I want to analyse microarray dataset (GSE38642) type HuGene-1_0-st-v1 in Bioconductor I follow the steps in this post http://bioinformatics.knowledgeblog.org/2011/06/20/analysing-microarray-data-in-bioconductor/ I struggled in Loading and normalising the data part celfiles <- read.affy(covdesc="phenodata.txt", path="data") I got this Error message

Warning messages:
1: In readLines(filename) : incomplete final line found on 'data/phenodata.txt'
2: The affy package can process data from the Gene ST 1.x series of arrays,
but you should consider using either the oligo or xps packages, which are specifically
designed for these arrays.

celfiles
AffyBatch object
size of arrays=1050x1050 features (45 kb)
cdf=HuGene-1_0-st-v1 (32321 affyids)
number of samples=63
number of genes=32321
annotation=hugene10stv1
notes=
Warning messages:
1: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘hugene10stv1cdf’ 
2: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘hugene10stv1cdf’ 

celfiles.gcrma <- gcrma(celfiles)
Adjusting for optical effect...............................................................Done.
Computing affinitiesError: length(prlen) == 1 is not TRUE

Does anyone know what is the problem or how can I change this command in R to get the results? Thanks in advance!

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