User: Andrew Einhorn

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8 years, 10 months ago
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8 years, 11 months ago
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Posts by Andrew Einhorn

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squaring each element of an expression set
... Using oligo to do rma, I end up with an expression set object whose elements are in log2 space. Is there some quick way to unlog (square) them to get absolute intensity values back? Andrew [[alternative HTML version deleted]] ...
oligo written 8.8 years ago by Andrew Einhorn80 • updated 8.8 years ago by Axel Klenk920
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histogram
... Hi there I would like to generate a histogramof my data after normalision using oligo rma. See code below. library(oligo) celfiles <- list.celfiles("cel_files",full.names = T) twfs <- read.celfiles(celfiles) results <- rma(twfs) hist(results) The hist implementation in this instance tak ...
written 8.8 years ago by Andrew Einhorn80 • updated 8.8 years ago by Wolfgang Huber13k
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gcrma hugene10st array
... Hi there I am trying to use gcrma to normalise a human gene st array data set. I read the following message from Feb 2010 that said that gcrma had not yet been implemented for the gene st arrays: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 7023/match=gcrma+hugene Is this ...
gcrma written 8.8 years ago by Andrew Einhorn80 • updated 8.8 years ago by Zhijin Wu260
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list of annaffy .db files?
... I am trying to use annaffy to annotate a hugene10stv1 array. I cannot find the name of the .db annotation packages I am supposed to install. My code thus far looks like: anncols <- aaf.handler()[c(1:4, 6,11)] anntable <- aafTableAnn(rownames(exprs(results))[1:50], "insert package name", ann ...
annotation annotate annaffy written 8.9 years ago by Andrew Einhorn80 • updated 8.9 years ago by Vincent J. Carey, Jr.6.3k
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superimpose lowess on smoothScatter
... I am trying to create an MvA plot using smoothScatter that has a lowess curve fit superimposed. I can't seem to find documentation on smoothScatter that will allow this. Currently I have: smoothScatter(x,y, main = "My MvA Plot") Can a lowess curve fit be added as an argument to smoothScatter? I ...
written 8.9 years ago by Andrew Einhorn80 • updated 8.9 years ago by Anderson, S. Keith30
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normalising with bad slides
... I have a set of 15 human gene st arrays that I am normalising. From analysis of the raw data, I can see that two of the slides are of very poor quality (signs of rna degradation, low pearson correlations etc). If I do an rma normalisation and include these two slides, will they effect the normalis ...
written 8.9 years ago by Andrew Einhorn80 • updated 8.9 years ago by Mark Cowley910
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boxplot labels vertical?
... i'm using the boxplot function on an affybatch object. it does the boxplot nicely, but because the labels are longish (5 chars), it doesn't print all of them out. i tried using the argument srt=90 but it's not working. any ideas why this is and/or how to fix it? Data <- ReadAffy() boxplot(Data ...
written 8.9 years ago by Andrew Einhorn80 • updated 8.9 years ago by Cei Abreu-Goodger830
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labeling affy histogram
... I am using the affy package to plot a histogram of raw data from an affymetrix dataset. Data <- ReadAffy() hist(Data[,1:4]) The histogram plots fine but I'd like to attach a legend to the plot, or at least label the plot-lines somehow. At present there is no way to discern which of the four li ...
affy written 8.9 years ago by Andrew Einhorn80 • updated 8.9 years ago by James W. MacDonald50k

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Popular Question 8.8 years ago, created a question with more than 1,000 views. For boxplot labels vertical?

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