[BioC] Illimina, BeadExplorer : getQC problem

[Nick Matigian]

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/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