User: Peter Davidsen

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Posts by Peter Davidsen

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Error when using the nsFilter command in the genefilter package
... Dear List, I'm trying to filter some microRNA expression data generated on the Affymetrix miRNA 2.0 array platform before running the DE genes analysis. However, I get an error when I apply the nsFilter function in the genefilter package - see below: #### my script #### #Set working dir setwd("C:/ ...
mirna annotation microrna biocinstaller written 7.4 years ago by Peter Davidsen210
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Answer: A: Error when using the nsFilter command in the genefilter package
... Dear List, I'm trying to filter some microRNA expression data generated on the Affymetrix miRNA 2.0 array platform before running the DE genes analysis. However, I get an error when I apply the nsFilter function in the genefilter package - see below: #### my script #### #Set working dir setwd("C:/ ...
written 7.4 years ago by Peter Davidsen210
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Problems creating a qPCRset object in "HTqPCR"
... Dear List, I'm trying to use the "HTqPCR" BioC package to analyze "SDS-format" qPCR data (ran 384-well plates on an ABI 7900HT). I have 20 different txt-files (in SDS-format) as I quantified 20 different miRNAs (thus, only one GOI per plate/file) - on each plate I have 33 samples in triplicate. Ex ...
htqpcr written 7.9 years ago by Peter Davidsen210
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Answer: A: Problems creating a qPCRset object in "HTqPCR"
... Dear List, I'm trying to use the "HTqPCR" BioC package to analyze "SDS-format" qPCR data (ran 384-well plates on an ABI 7900HT). I have 20 different txt-files (in SDS-format) as I quantified 20 different miRNAs (thus, only one GOI per plate/file) - on each plate I have 33 samples in triplicate. Ex ...
written 7.9 years ago by Peter Davidsen210
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Comment: C: lmFit only deals with numerical values (data matrix object)?
... Hi Sean, I read it, but wasn't 100% sure! Okay, as microarray data need to be log-transformed in order to compare gene activities - Could I then, if I want to use the lmFit function in limma: 1) transform all my log2 ratio data in my data matrix into fold change - 2^(log2 ratio) 2 divide fold chan ...
written 8.0 years ago by Peter Davidsen210 • updated 4.3 years ago by Gordon Smyth37k
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Comment: C: lmFit only deals with numerical values (data matrix object)?
... Hi Sean, I read it, but wasn't 100% sure! Okay, as microarray data need to be log-transformed in order to compare gene activities - Could I then, if I want to use the lmFit function in limma: 1) transform all my log2 ratio data in my data matrix into fold change - 2^(log2 ratio) 2 divide fold chan ...
written 8.0 years ago by Peter Davidsen210 • updated 4.3 years ago by Gordon Smyth37k
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Comment: A: lmFit only deals with numerical values (data matrix object)?
... Hi List Does "lmFit" in limma only deals with numeric values (positive numbers)? I have created a data matrix object with log2 ratio data (some data assume negative values). Can I use my data matrix as object in the lmFit function? Kind regards Peter ...
written 8.0 years ago by Peter Davidsen210 • updated 4.3 years ago by Gordon Smyth37k
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lmFit only deals with numerical values (data matrix object)?
... Hi List Does "lmFit" in limma only deals with numeric values (positive numbers)? I have created a data matrix object with log2 ratio data (some data assume negative values). Can I use my data matrix as object in the lmFit function? Kind regards Peter ...
limma lmfit written 8.0 years ago by Peter Davidsen210 • updated 4.3 years ago by Gordon Smyth37k
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Answer: A: How to read in log2 ratio data
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written 8.0 years ago by Peter Davidsen210
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How to read in log2 ratio data
... Hi all, I would like to conduct a time-course analysis using the limma package on my chip data (run as dual-color). I have two classes/groups with 8 subjects in each. Each 'experimental unit' has been measured at three different time points. However, I already have all the data as lowess normalized ...
probe limma written 8.0 years ago by Peter Davidsen210

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