Question: How to bypass ReadAffy warning
0
gravatar for joseph.a.white1
14 months ago by
joseph.a.white10 wrote:

Hello,

The Affydata package ReadAffy () method throws up a warning when I try to process CEL files from Gene ST 1.0 arrays.  

Yes, I read the WARNING.  I would like to use the ReadAffy method.  Does anyone know how to bypass the warning--since, you know, its a warning.  I did attempt to suppress warnings and shut them off entirely to no avail.  Is there some way to bypass this roadblock?  

 

Thanks,

jw

 

affy • 310 views
ADD COMMENTlink modified 13 months ago • written 14 months ago by joseph.a.white10
Answer: How to bypass ReadAffy warning
0
gravatar for James W. MacDonald
14 months ago by
United States
James W. MacDonald50k wrote:

Can you explain how a warning is a roadblock? You have simply been warned that the affy package wasn't ever intended for use with the array you are using. Anyway, you show no code so it's impossible to say where you might have gone wrong. But I have no such problems:

> dat <- ReadAffy(filenames = dir()[1:3])
Warning message:

The affy package can process data from the Gene ST 1.x series of arrays,
but you should consider using either the oligo or xps packages, which are specifically
designed for these arrays.

> dat <- suppressWarnings(ReadAffy(filenames =dir()[1:3]))
> rma(dat)
Background correcting
Normalizing
Calculating Expression
ExpressionSet (storageMode: lockedEnvironment)
assayData: 28826 features, 3 samples 
  element names: exprs 
protocolData
  sampleNames: MKE_B10.CEL MKE_B11.CEL MKE_B12.CEL
  varLabels: ScanDate
  varMetadata: labelDescription
phenoData
  sampleNames: MKE_B10.CEL MKE_B11.CEL MKE_B12.CEL
  varLabels: sample
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
Annotation: ragene10stv1 

So yes, you do get a warning, which can be silenced using suppressWarnings, and in the end you get summarized data in an ExpressionSet just like you appear to want.

ADD COMMENTlink modified 14 months ago • written 14 months ago by James W. MacDonald50k
Answer: How to bypass ReadAffy warning
0
gravatar for joseph.a.white1
13 months ago by
joseph.a.white10 wrote:

Hi ,

You're right.  The following is from an R session:  When I saw no objects, I assumed R did not process the command.  

Sorry, I should have looked into it further.  

Thanks for the example. 

Cheers,

jw

================================================

> library("affydata")
Loading required package: affy
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
[ ... ]
> setwd("__MACOSX")
> dir()
[1] "0112F-02_A18_(MoGene-1_0-st-v1).CEL"
[2] "0112F-02_A28_(MoGene-1_0-st-v1).CEL"
[3] "0112F-02_A32_(MoGene-1_0-st-v1).CEL"
[4] "0112F-02_A36_(MoGene-1_0-st-v1).CEL"
[5] "0112F-02_A44_(MoGene-1_0-st-v1).CEL"
[6] "0112F-02_F52_(MoGene-1_0-st-v1).CEL"
[7] "0112F-02_F58_(MoGene-1_0-st-v1).CEL"
[8] "0112F-02_F60_(MoGene-1_0-st-v1).CEL"
[9] "0112F-02_F64_(MoGene-1_0-st-v1).CEL"
[10] "0112F-02_F66_(MoGene-1_0-st-v1).CEL"
[11] "0112F-02_F74_2_(MoGene-1_0-st-v1).CEL"
[12] "0112F-02_V1_(MoGene-1_0-st-v1).CEL"   
[13] "0112F-02_V3_(MoGene-1_0-st-v1).CEL"   
[14] "0112F-02_V4_(MoGene-1_0-st-v1).CEL"   
[15] "0112F-02_V5_(MoGene-1_0-st-v1).CEL"   
[16] "0112F-02_V6_(MoGene-1_0-st-v1).CEL"   
[17] "0112F-02_V7_(MoGene-1_0-st-v1).CEL"   
> y <- ReadAffy()
Warning message:
The affy package can process data from the Gene ST 1.x series of arrays,
but you should consider using either the oligo or xps packages, which are specifically
designed for these arrays.

===============================================

ADD COMMENTlink modified 13 months ago by Gordon Smyth37k • written 13 months ago by joseph.a.white10

In R, an "Error" message always means that the operation has been stopped because of incorrect inputs or an illegal operation. By contrast, a "Warning message" always means the operation has run through to completion. The purpose of a warning message is to alert the user about something that is unusual, so the user can make a judgement call for themselves to decide whether they want to use the results. Users are assumed to have the expertise to make this judgement.

New users of R and Bioconductor often overlook the distinction between errors and warnings, so it's something we often have to point out on this support site. You shouldn't assume we are being rude to users when we do that. I've lost count of the number of times people have asked "why didn't my code run" and we have had to answer "but it did".

Note also that most R functions complete quietly. When you assign the output from an R function into a new object (as in y <- ReadAffy) you won't "see" any output unless you explicitly examine y using show(y) or summary(y) or whatever.

Hope this helps.

ADD REPLYlink modified 13 months ago • written 13 months ago by Gordon Smyth37k
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