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7364256
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2011-09-09T15:51:03.370
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2016-11-13T08:48:55.387
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2016-11-13T08:48:55.387
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text
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The correct place for this question is on the <a href="https://support.bioconductor.org" rel="nofollow noreferrer">Bioconductor</a> support site. It's better to provide a reproducible example that captures the essence of the problem; creating the reproducible example often helps to identify the reason for the problem. <pre><code>library(Biobase) exprs <- matrix(0, nrow=5, ncol=3, dimnames=list(letters[1:5], LETTERS[1:3])) pData <- data.frame(id=c("foo", "bar", "baz"), row.names=c("x", "y", "z")) phenoData <- AnnotatedDataFrame(data=pData) </code></pre> leading to <pre><code>> ExpressionSet(exprs, phenoData=phenoData) Error in validObject(.Object) : invalid class "ExpressionSet" object: sampleNames differ between assayData and phenoData </code></pre> The problem is that the <code>colname</code> of <code>exprs</code> (i.e., the names of the samples in the experiment) differ frrom the <code>row.names</code> of <code>pData</code> (i.e., the description of the samples) <pre><code>> row.names(pData) [1] "x" "y" "z" > colnames(exprs) [1] "A" "B" "C" </code></pre> and the solution is to make them the same <pre><code>> colnames(exprs) <- row.names(pData) > eset <- ExpressionSet(exprs, phenoData=phenoData) > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 5 features, 3 samples element names: exprs protocolData: none phenoData sampleNames: x y z varLabels: id varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: </code></pre> Additional elements can be added to an existing ExpressionSet using <code>assayDataReplace()</code>, e.g., <pre><code>> assayDataElement(eset, "foo") <- sqrt(exprs) > eset ExpressionSet (storageMode: lockedEnvironment) assayData: 5 features, 3 samples element names: exprs, foo protocolData: none phenoData sampleNames: x y z varLabels: id varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: </code></pre> or from the start <pre><code>> env = new.env() > env$exprs = exprs > env$sqrt = sqrt(exprs) > lockEnvironment(env) > ExpressionSet(env, pData=pData) ExpressionSet (storageMode: environment) assayData: 5 features, 3 samples element names: exprs, sqrt protocolData: none phenoData: none featureData: none experimentData: use 'experimentData(object)' Annotation: </code></pre>
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1. This table or related slice is empty.
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1. POExpressionset - phenodata
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1. USMartin Morgan
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1. USMartin Morgan
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1. COThanks Dr. Morgan, it worked. Greatly appreciate your help.
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 USAvin

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