Question: problem of codelink
1
gravatar for fang_zhuo
4.8 years ago by
fang_zhuo10
fang_zhuo10 wrote:

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

codelink • 640 views
ADD COMMENTlink modified 4.8 years ago by Diego Diez750 • written 4.8 years ago by fang_zhuo10

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.

 

ADD REPLYlink written 4.8 years ago by Diego Diez750
Answer: problem of codelink
0
gravatar for Diego Diez
4.8 years ago by
Diego Diez750
Japan
Diego Diez750 wrote:

Dear Minnie,

I understand you downloaded the codelink data 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. For example:

library(GEOquery)
eset <- getGEO("GSE24807")[[1]]
ADD COMMENTlink written 4.8 years ago by Diego Diez750
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