User: David Westergaard

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Posts by David Westergaard

<prev • 28 results • page 3 of 3 • next >
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Comment: C: arrayQualityMetrics error and question
... Hi, I did not express myself clearly enough - I actually didn't have trouble with beadarray. The package giving me trouble was Cairo, but I solved that by installing newest cairoDevice pacakge, followed by Cairo-1.4-5. I'm now running R-2.14 with arrayQualityMetrics v3.10 - I'll let you know if I e ...
written 7.4 years ago by David Westergaard280
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Comment: C: arrayQualityMetrics error and question
... Hi Wolfgang, The problem hasn't really resolved itself. I can't update any further, since I'm having trouble installing arrayQualityMatrics with R-2.14 on the server I have access to. (beadarray, which is a requirement, needs R>=2.13) Cairo fails to install, giving two errors: cairotalk.c:894: e ...
written 7.4 years ago by David Westergaard280
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arrayQualityMetrics error and question
... Hello, I am trying to use the BioC package arrayQualityMetrics to asses the quality of a range of experiments. I am, however, running into errors, when processing Affymetrix Hugene designs, particularly http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33443 I'm using the following code: libra ...
cdf arrayqualitymetrics written 7.4 years ago by David Westergaard280 • updated 7.4 years ago by Wolfgang Huber13k
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Summarizing Single-channel Agilent data
... Hello, I am working on normalizing raw data from http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-33005 using the Limma package. Following "standard" procedure, I do background correction, and then normalize: # Read target from file targets <- readTargets("targets") RG <- read.maimages( ...
go written 7.4 years ago by David Westergaard280 • updated 7.4 years ago by Axel Klenk930
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Answer: A: Odd warning in simpleaffy, using quality control
... Hi Maciej, The cdf package is installed and working. (I've been preprocessing the same datafiles using 'affy') I still (almost) the same error: Attaching package: 'hugene10stv1cdf' The following object(s) are masked from 'package:hgu133plus2cdf': i2xy, xy2i Error: NAs in foreign function ca ...
written 7.4 years ago by David Westergaard280
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Odd warning in simpleaffy, using quality control
... Hello, I'm trying to run some quality control (qc) on a bunch of raw files retrieved from ArrayExpress, using simpleaffy, with the code: mixture.batch <- ReadAffy() mixture.qc <- qc(mixture.batch) However, when I get to an experiment which has not used the "hgu133plus2cdf" platform (In th ...
cdf simpleaffy arrayexpress written 7.4 years ago by David Westergaard280
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Comment: C: Siggenes SAM analysis: log2 transformation and Understanding output
... Hi Jim, Thank you for your thorough answers. Just to make it absolutely clear: p0 is the chance that a randomly picked gene is differentially expressed, when picking a gene from the WHOLE data set? Secondly, should I be wary of p0 values below/above some threshold? I am working on multiple data se ...
written 7.4 years ago by David Westergaard280
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Siggenes SAM analysis: log2 transformation and Understanding output
... Hello, I am currently working on a data set about kiwi consumption for my bachelors project. The data is available at http://www.ebi.ac.uk/arrayexpress/experiments/E-MEXP-2030 I'm abit confused as to how to interpret the output parameters, specifically p0. I've run the following code: dataset < ...
written 7.4 years ago by David Westergaard280 • updated 7.4 years ago by James W. MacDonald50k

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