Error with boxplot command from oligo package with raw Affy data
2
0
Entering edit mode
@johnleejohnson-7785
Last seen 5.1 years ago
United States

Hello, I am very new to analyzing microarray data and could use some help. I am trying to read in celfiles and plot a boxplot of the probe intensities, but I'm running into a problem. Any help is greatly appreciated! These are the commands I'm running:

library(GEOquery)
library(oligo)
library(limma)
source("https://bioconductor.org/biocLite.R")
#Install annotation
biocLite("pd.hugene.1.0.st.v1")
library(pd.hugene.1.0.st.v1)
getGEOSuppFiles("GSE52882")
#Untar GEO tar file in shell
celFilelist = list.celfiles("GSE52882", full.name=T)[1:6]
affyRaw=read.celfiles(celFiles)
boxplot(affyRaw)

The error I'm getting is:

Error in match.arg(target, c("probeset", "core", "full", "extended")) : 
  'arg' should be one of “probeset”, “core”, “full”, “extended”

Traceback returns:

14: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices), 
        collapse = ", ")), domain = NA)
13: match.arg(target, c("probeset", "core", "full", "extended"))
12: stArrayPmInfo(object, target = target, sortBy = NULL)
11: .local(object, ...)
10: pmindex(getPlatformDesign(object), subset = subset, target = target)
9: pmindex(getPlatformDesign(object), subset = subset, target = target)
8: .local(object, ...)
7: pmindex(x, target = target)
6: pmindex(x, target = target)
5: getProbeIndex(x, type = which, target = target)
4: unique(getProbeIndex(x, type = which, target = target))
3: .local(x, ...)
2: boxplot(affyRaw)
1: boxplot(affyRaw)

affyRaw seems to be correct:

 

affyRaw
​GeneFeatureSet (storageMode: lockedEnvironment) assayData: 1102500 features, 6 samples element names: exprs protocolData rowNames: GSM1277464_bh20130307hg10_07_A375P31_773_HuGene-1_0-st-v1_.CEL GSM1277465_bh20130307hg10_08_A375P32_773_HuGene-1_0-st-v1_.CEL ... GSM1277469_bh20130307hg10_12_A375PLX33_773_HuGene-1_0-st-v1_.CEL (6 total) varLabels: exprs dates varMetadata: labelDescription channel phenoData rowNames: GSM1277464_bh20130307hg10_07_A375P31_773_HuGene-1_0-st-v1_.CEL GSM1277465_bh20130307hg10_08_A375P32_773_HuGene-1_0-st-v1_.CEL ... GSM1277469_bh20130307hg10_12_A375PLX33_773_HuGene-1_0-st-v1_.CEL (6 total) varLabels: index varMetadata: labelDescription channel featureData: none experimentData: use 'experimentData(object)' Annotation: pd.hugene.1.0.st.v1

<font face="monospace">And my session info is:</font>

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.12.4 (unknown)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] pd.hugene.1.0.st.v1_3.14.1 DBI_0.6-1                 
 [3] RSQLite_1.1-2              limma_3.26.9              
 [5] oligo_1.34.2               Biostrings_2.38.4         
 [7] XVector_0.10.0             IRanges_2.4.8             
 [9] S4Vectors_0.8.11           oligoClasses_1.32.0       
[11] GEOquery_2.36.0            Biobase_2.30.0            
[13] BiocGenerics_0.16.1       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10               affxparser_1.42.0         
 [3] splines_3.2.3              GenomicRanges_1.22.4      
 [5] zlibbioc_1.16.0            bit_1.1-12                
 [7] foreach_1.4.3              GenomeInfoDb_1.6.3        
 [9] tools_3.2.3                SummarizedExperiment_1.0.2
[11] ff_2.2-13                  iterators_1.0.8           
[13] digest_0.6.12              preprocessCore_1.32.0     
[15] affyio_1.40.0              bitops_1.0-6              
[17] codetools_0.2-15           RCurl_1.95-4.8            
[19] memoise_1.0.0              BiocInstaller_1.20.3      
[21] XML_3.98-1.6
oligo • 2.2k views
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1
Entering edit mode

I don't want to say something wrong as I am myself also a beginner, but I think the problem lies that to use the boxplot fonction of oligo, you need to use data coming from the oligo::rma (even if not normalized yet), because you need to select the "Level of summarization (only for Exon/Gene arrays)" (see ?oligo::rma and the oligo user guide). That what the error message explains you.

Here is an example, where I worked on the gene level (see the target="core") :

#boxplot pre rma
data.core <- oligo::rma(affyRAW, background=FALSE, normalize=FALSE, subset=NULL, target="core")
par(mar = c(10,4,4,2) + 0.1)
oligo::boxplot(data.core, las = 2)
mtext(text="log2 Intensity", side=2, line=2.5, las=0)  

This might help you.

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0
Entering edit mode
@johnleejohnson-7785
Last seen 5.1 years ago
United States

Yes, that was it! Thanks so much

I did not realize you had to choose the level of summarization. For example, putting this command works,

boxplot(affyRaw, target="core")
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 14 hours ago
United States

This is a bit cryptic, as it's not really explained in the help page. In other words, the help page says this:

     ## S4 method for signature 'FeatureSet'
     boxplot(x, which=c("pm", "mm", "bg", "both", "all"), transfo=log2, nsample=10000, ...)
    

Which doesn't say anything about the target argument. However, if you look at the function body,

> showMethods(boxplot, class = "FeatureSet", includeDefs=T)
Function: boxplot (package graphics)
x="FeatureSet"
function (x, ...)
{
    .local <- function (x, which = c("pm", "mm", "bg", "both",
        "all"), transfo = log2, nsample = 10000, target = "mps1",
        ...)
   <snip>

You can see that there is this argument target = "mps1". And you don't have any mps1 targets, you just have "core" and "probeset". So you need to do

boxplot(affyRaw, target = "core")
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0
Entering edit mode

Well, I also learned something then, it's much easier this way

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