Dear Minnie,
Thanks for your interest in the codelink package. May I suggest that you post your question in the Bioconductor support site?
(https://support.bioconductor.org) This way other users may benefit from this exchange.
I get you downloaded the that from GEO? The problem is that the data there (at least for this dataset) is not the originally exported Codelink data- hence codelink cannot read it. You can try and download the data using the GEOquery Bioconductor package instead. The data will load as an ExpressionSet object.
Best,
Diego
On Sat, Feb 28, 2015 at 3:24 PM, ZHUO Minnie FANG <fang_zhuo@lilly.com> wrote:
> Dear Dr. Diez,
>
>
>
> I am using your package “codelink ” to analyze GE arrays (GSE24807).
> But I cannot read the raw files. The error msg was:
>
>
>
> Error in readHeader(files[n], dec = TRUE) : Not a Codelink exported file.
>
> In addition: Warning messages:
>
> 1: The Codelink interface is deprecated. Read Codelink data with
> 'readCodelinkSet' instead. More details in the vignette and documentation.
>
> 2: In .readCodelinkRaw(files = files, sample.name = sample.name, flag
> = flag, :
>
> 'readCodelink' and 'readCodelinkSet' do not convert intensities to
> NA based on flags anymore, except for spots flagged as 'M' (MSR spot).
> Instead,
> createWeights() is used to assign weights. These weights can be used
> during normalization and linear modeling. To obtain the old behavior
> use parameter 'old=TRUE' (weights will be created anyway).
>
>
>
> Here is the head of my input file:
>
>
>
> ######### File start #########
>
>
>
> CodeLink<99> Expression Analysis 4.1.0.29054
>
> Analysis Report Name: Expression Report
>
> Image File Name: T00294628_635.tif
>
> Analysis Date and Time: 11/30/2005 14:07
>
> GEN file name: EXP294X192-912.22.GEN Product: Human Whole Genome
>
> Normalization Method: Median-Normalization
>
> Computation Method for Median: Spot Based
>
> Threshold Trim Percentage: 20
>
> Array 1
>
> Raw TrimMean Negative Control 39.02883411
>
> Normalized TrimMean Negative Control 0.392078287
>
> Median 99.54347229
>
> Sample Name Sample001
>
>
>
>
>
>
>
>
>
>
>
> Idx Array ACCN# Probe_Name Type Raw_Intensity
> Normalized_Intensity Quality Flag Description
>
> 1 1 ARAB GE1071362 POSITIVE 1279.835449
> 12.85705049 G NULL
>
> 2 1 ARAB GE1071362 POSITIVE 1643.883057
> 16.51422257 G NULL
>
> 3 1 ARAB GE1071362 POSITIVE 1779.678955
> 17.87840944 G NULL
>
> 4 1 ARAB GE1071362 POSITIVE 1968.317017
> 19.77344141 G NULL
>
> 5 1 ARAB GE1071362 POSITIVE 1708.451172
> 17.16286495 G NULL
>
> 6 1 ARAB GE1071362 POSITIVE 1440.529419
> 14.47135996 G NULL
>
>
>
> ######### File end #########
>
>
>
> Do you know what is the problem? Many thanks in advance!
>
>
>
> Best regards,
>
>
>
> Minnie
Dear Minnie, thank you for taking the time to bring this to the support site. May I suggest that you put your post in a question format? That is, please remove the part of the conversation that is my answer and I will post that as a answer to the question.