Hi
Sorry for the previous empty messages, hope this works now.
I have been getting the same error, I have run the same csv file and
code
using a older version of R,does anybody know how to fix?
> DATA<-readBead("Illumina Trial Ref-
6v2_Sample_Probe_Profile_Nonorm.csv",
annotation="Trial");
Read Illumina Trial Ref-6v2_Sample_Probe_Profile_Nonorm.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
Thanks
Nick
---------------------------------------------------------------------
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="" bea="" de="" 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
