User: Peter Davidsen

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Posts by Peter Davidsen

<prev • 20 results • page 1 of 2 • next >
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Answer: A: Is a subset of my arrays from degraded RNA?
... Dear List, Although I do realise that my question has more to do with actual data interpretation that coding using BioC packages, I'm hoping for some input from other users with experience in microarray data analysis. I order to support my explanation below, I have made a pdf with diagnostic plots ...
written 4.7 years ago by Peter Davidsen210
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Is a subset of my arrays from degraded RNA?
... Dear List, Although I do realise that my question has more to do with actual data interpretation that coding using BioC packages, I'm hoping for some input from other users with experience in microarray data analysis. I order to support my explanation below, I have made a pdf with diagnostic plots ...
microarray go clustering affy affyplm simpleaffy written 4.7 years ago by Peter Davidsen210
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pathview - plotting multiple samples in the same graph?
... Dear List, I recently decided to give the pathview package a try as I would like to map multiple samples data on the same pathway (ie a given node/gene in a KEGG pathway can consist of more than one color). After reading the vignette "Pathview: pathway based data integration and visualization" (ver ...
pathways go pathview written 5.1 years ago by Peter Davidsen210
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Answer: A: pathview - plotting multiple samples in the same graph?
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written 5.1 years ago by Peter Davidsen210
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How to retrieve all GO terms at level 5 as well as their annotated genes
... Dear list, I'm looking for a way to get the names of all Gene Ontology terms for Biological Processes at level 5 as well as the genes (human gene symbols) annotated to each of the level 5 GO terms. I have tried to query the DAVID knowledgebase, but the online tool doesn't seem to respond to any re ...
go written 5.8 years ago by Peter Davidsen210
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Answer: A: How to retrieve all GO terms at level 5 as well as their annotated genes
... Dear list, I'm looking for a way to get the names of all Gene Ontology terms for Biological Processes at level 5 as well as the genes (human gene symbols) annotated to each of the level 5 GO terms. I have tried to query the DAVID knowledgebase, but the online tool doesn't seem to respond to any re ...
written 5.8 years ago by Peter Davidsen210
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Most diff exp genes are up-regulated... can this be true?
... Dear List, I'm analysing some one-color microarray data generated using a custom designed Agilent array (their 8 x 60K platform). When I compare control samples to treated ones most (i.e. >80%) of the differentially expressed transcripts are up-regulated. This pronounced up-regulation is indepen ...
microarray normalization vsn limma siggenes written 6.3 years ago by Peter Davidsen210
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Answer: A: Most diff exp genes are up-regulated... can this be true?
... Dear List, I'm analysing some one-color microarray data generated using a custom designed Agilent array (their 8 x 60K platform). When I compare control samples to treated ones most (i.e. >80%) of the differentially expressed transcripts are up-regulated. This pronounced up-regulation is indepen ...
written 6.3 years ago by Peter Davidsen210
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Answer: A: Error using impute.knn function
... Dear List, After quantile normalizing some Agilent microarray data I end up with a data matrix containing missing values (as I choose to log2 transform my matrix just before the normalization step). Thus, I want to use the impute.knn() function in the impute package... however, I keep getting an er ...
written 6.7 years ago by Peter Davidsen210
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Error using impute.knn function
... Dear List, After quantile normalizing some Agilent microarray data I end up with a data matrix containing missing values (as I choose to log2 transform my matrix just before the normalization step). Thus, I want to use the impute.knn() function in the impute package... however, I keep getting an er ...
microarray normalization impute written 6.7 years ago by Peter Davidsen210

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