Question: Error in arrayQualityMetrics
0
gravatar for peirinl
19 months ago by
peirinl0
peirinl0 wrote:

I am running the workflow "An end to end workflow for differential gene expression using Affymetrix microarrays ".

pData(raw_data) <- pData(raw_data)[, c("Source.Name",
                                       "Characteristics.individual.",
                                       "Factor.Value.disease.",
                                       "Factor.Value.phenotype.")]

exp_raw <- log2(exprs(raw_data))

PCA_raw <- prcomp(t(exp_raw), scale = FALSE)

dataGG <- data.frame(PC1 = PCA_raw$x[,1], PC2 = PCA_raw$x[,2],
                     Disease = pData(raw_data)$Factor.Value.disease.,
                     Phenotype = pData(raw_data)$Factor.Value.phenotype.,
                     Individual = pData(raw_data)$Characteristics.individual.)

arrayQualityMetrics(expressionset = raw_data,
                    outdir = "Report_for_Palmieri_raw",
                    force = TRUE, do.logtransform = TRUE,
                    intgroup = c("Factor.Value.disease.","Factor.Value.phenotype."))

Result:

The directory 'Report_for_Palmieri_raw' has been created.

Error in colnames(pd) %in% intgroup : argument "intgroup" missing,with no default value

What could cause this problem?

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

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

arrayqualitymetrics • 353 views
ADD COMMENTlink modified 19 months ago by Mike Smith3.6k • written 19 months ago by peirinl0

session info

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

ADD REPLYlink written 19 months ago by peirinl0
Answer: Error in arrayQualityMetrics
1
gravatar for Mike Smith
19 months ago by
Mike Smith3.6k
EMBL Heidelberg / de.NBI
Mike Smith3.6k wrote:

I'm not sure why this hadn't been detected before, but there seemed to be problem passing the intgroup argument to one of the internal functions.  I've patched this in version arrayQualityMetrics version 3.33.4

This will take a few days to appear in the Bioconductor system, but you can install it now with

BiocInstaller::biocLite('grimbough/arrayQualityMetrics')
ADD COMMENTlink written 19 months ago by Mike Smith3.6k

It works! Thank you very much.

ADD REPLYlink written 19 months ago by peirinl0
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