User: Hoyles, Lesley

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6 years, 12 months ago
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7 years, 3 months ago
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l**************@imperial.ac.uk

Posts by Hoyles, Lesley

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Query regarding Heatplus
... Hi I've used Heatplus to create heatmaps from my single-channel Agilent data. However, I have a couple of simple queries in relation to the legends associated with the figures. In figure 1 of the vignette for Heatplus (http://www.bioconductor.org/ packages/release/bioc/vignettes/Heatplus/inst/doc/ ...
heatplus written 7.0 years ago by Hoyles, Lesley50
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Comment: C: Assigning gene symbols to Affymetrix data and averaging probes
... Hi Jim Thanks, the reannotation worked a treat. I've been able to export the normalized data in annotated format. I am adverse to removing probes that have no Entrez ID associated with them as I want to put the whole set of data through limma. I can't use the annotated expr.loess in lmFit, but is ...
written 7.1 years ago by Hoyles, Lesley50
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Assigning gene symbols to Affymetrix data and averaging probes
... Hi I have processed my affy data and am able to annotate the object mice.loess using the following. ID <- featureNames(mice.loess) Symbol <- getSYMBOL(ID,'mouse4302.db') fData(mice.loess) <- data.frame(ID=ID,Symbol=Symbol) However, when I convert my object as follows - expr.loess <- e ...
annotation annotate affy limma convert written 7.1 years ago by Hoyles, Lesley50 • updated 7.1 years ago by James W. MacDonald51k
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Comment: C: Confirming a batch effect has been removed
... Hi Jim Thanks so much for the feedback. It's been very helpful. >The only issue would arise if say score_1 samples are only found in >batch 1 and score_0 samples are only found in batch 2. Thankfully, I don't have that problem with my data. Best wishes Lesley _____________________________ ...
written 7.3 years ago by Hoyles, Lesley50
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Confirming a batch effect has been removed
... Hi I am working with single-channel Agilent data. I have two batches of microarrays for biopsies from different patients (batch 1, 25 arrays; batch 2, 34 arrays). There are no replicate samples for any of the patients in either of the batches. The patients are classified according to disease score. ...
written 7.3 years ago by Hoyles, Lesley50 • updated 7.3 years ago by James W. MacDonald51k

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