User: peirinl

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peirinl0
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Posts by peirinl

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Comment: C: Error when restore rownames of Feature data of ExpressionSet
... I try another dataset, also using hgu133plus2.db. The outcome is same.  ...
written 21 months ago by peirinl0
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Comment: C: Error when restore rownames of Feature data of ExpressionSet
... Nice! So I can use anno_dataSet to do the subsequent LIMMA testing? ...
written 21 months ago by peirinl0
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Comment: C: Error when restore rownames of Feature data of ExpressionSet
... You are right, the duplication is induced by left_join. Before left_join,  > anyDuplicated(rownames(fData(dataSet_final))) [1] 0 > anyDuplicated(anno_dataSet$PROBEID) [1] 2 > rownames(fData(riester_final))[28589] [1] "227321_at" > rownames(fData(riester_final))[28588] [1] "227320_at" ...
written 21 months ago by peirinl0
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Error when restore rownames of Feature data of ExpressionSet
... Dear all, I do annotation and removing multiple mappings,  anno_dataSet <- AnnotationDbi::select(hgu133plus2.db, keys=(featureNames(dataSet_filtered)), columns = c("SYMBOL", "GENENAME"), ...
expressionset written 21 months ago by peirinl0 • updated 21 months ago by Martin Morgan ♦♦ 23k
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Comment: C: Error in arrayQualityMetrics
... It works! Thank you very much. ...
written 21 months ago by peirinl0
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Comment: C: Error in arrayQualityMetrics
... session info attached base packages: [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     ...
written 21 months ago by peirinl0
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Error in arrayQualityMetrics
... 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.dise ...
arrayqualitymetrics written 21 months ago by peirinl0 • updated 21 months ago by Mike Smith3.8k
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Comment: C: function getAE from ArrayExpress needs update because EBI has switched to https
... Thanks, I managed to edit getAE.R using trace("getAE.R", edit=TRUE). I simply copy and paste your function. Thank you.  ...
written 21 months ago by peirinl0
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prcomp show "Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded"
... I am running a microarray data analysis,      raw_data = read.celfiles(....... )     exp_raw <- log2(exprs(raw_data))      PCA_raw <- prcomp(t(exp_raw), scale = FALSE) but I got an error,     Error in La.svd(x, nu, nv) : LAPACK routines cannot be loaded     Besides: Warning message:     ...
affymetrix microarrays prcomp written 21 months ago by peirinl0 • updated 21 months ago by James W. MacDonald50k
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Comment: C: function getAE from ArrayExpress needs update because EBI has switched to https
... Sorry, could you please tell me, or point me to a reference, how to fix a .R file such as getAE.R? ...
written 21 months ago by peirinl0

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