Hello

We are trying to analyse some Illumina chips. We have installed
BeadExplorer_1.2.0.zip
<http://bioconductor.org/packages/2.0/bioc/bin/windows/contrib/2.5/BeadE
xplorer_1.2.0.zip>   .  The  BeadStudio version of our datafiles 1.5. 
We followed the Vignette.
 
we do the following:  

	data<-readBead("060027_PMT 585_gene_profile.csv")
	Read 060027_PMT 585_gene_profile.csv
	Error in data.frame(sample = 1:length(sampleNames), row.names =
sampleNames) : 
	        row names supplied are of the wrong length
	In addition: Warning message:
	read.phenoData is deprecated, use read.AnnotatedDataFrame
instead 
	> dir()
	[1] "060027_PMT 585_gene_profile.csv"       "060027_PMT
585_gene_profile.txt"       "060027_PMT 585_qcinfo.csv"            
	[4] "060027_PMT 585_qcinfo.txt"             "060027_PMT
585_short_gene_profile.txt" "BeadExplorer"                         
	[7] "qcinfo_headers.txt"      

 
 
Then we tried with tab delimited 

	> data<-readBead("060027_PMT 585_gene_profile.txt")
	Read 060027_PMT 585_gene_profile.txt
	Warning messages:
	1: read.phenoData is deprecated, use read.AnnotatedDataFrame
instead 
	2: The phenoData class is deprecated, use AnnotatedDataFrame
(with ExpressionSet) instead 
	3: The exprSet class is deprecated, use ExpressionSet instead 
	4: The exprSet class is deprecated, use ExpressionSet instead 
	5: The exprSet class is deprecated, use ExpressionSet instead 
	6: The exprSet class is deprecated, use ExpressionSet instead 
	7: The exprSet class is deprecated, use ExpressionSet instead 
	8: The exprSet class is deprecated, use ExpressionSet instead 
	9: The exprSet class is deprecated, use ExpressionSet instead 
	10: The exprSet class is deprecated, use ExpressionSet instead 
	>data
	Expression Set (exprSet) with 
	        47293 genes
	        9 samples
	        phenoData object with 1 variables and 9 cases
	        varLabels
	                sample: arbitrary numbering
	Warning messages:
	1: The exprSet class is deprecated, use ExpressionSet instead 
	2: The exprSet class is deprecated, use ExpressionSet instead 
	3: The phenoData class is deprecated, use AnnotatedDataFrame
(with ExpressionSet) instead 
	 

but: 
 

	> qcdata<-getQC(data)
	Error in `row.names<-.data.frame`(`*tmp*`, value =
c("A.sister.avant.confluence",  : 
	        invalid 'row.names' length
	 

 
 
First line of  qc file: 060027_PMT 585_qcinfo.txt 

Illumina Inc. BeadStudio version 1.5.0.34

Normalization = none

Array Content = Human_WG-6.xml

Error Model = none

DateTime = 30/5/2006 09:51

Local Settings = sv-FI

 
 
First line of data files 060027_PMT 585_gene_profile.txt"
 
Illumina Inc. BeadStudio version 1.5.0.34

Normalization = none

Array Content = Human_WG-6.xml

Error Model = none

DateTime = 30/5/2006 09:51

Local Settings = sv-FI

 

ArrayID

1508893068_A    etc 

1508893068_B

1508893068_C

1508893068_D

1508893068_E

1508893068_F

1508893069_E

1508893069_F

1508893075_E

 
 
Thank you in advance 
 
Johanne Duhaime
IRCM
 

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