User: David Westergaard

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Posts by David Westergaard

<prev • 28 results • page 2 of 3 • next >
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Printing arrayQualityMetrics report
... Hello, I am trying to include an arrayQualityMetrics report in my appendix, but I am finding it very difficult to produce a pretty version as a pdf. I have tried simply to print to file in both Google Chrome and Iceweasel, and both of them are having trouble placing the figures correctly in the pdf ...
convert arrayqualitymetrics written 7.3 years ago by David Westergaard280 • updated 7.3 years ago by Wolfgang Huber13k
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Answer: A: biomaRt installation error ??
... Dear Alyaa, It seems your problem is related to RCurl, and not the biomaRt package. A quick google search on 'Cannot find curl-config' seems to return a very relevant hit: http://www.omegahat.org/RCurl/FAQ.html Could you try this, and then try installing RCurl again? Best, David 2012/6/16 Alyaa ...
written 7.3 years ago by David Westergaard280
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Answer: A: Microarray experiment design issues
... Hi Ali, I don't think this list is appropriate to answer these questions, since it doesn't generally involve any bioconductor packages. However, I don't really see why you would have a problem in A. Are both cell lines not exposed to the same variation in humidty levels, temperature, oxygen levels ...
written 7.3 years ago by David Westergaard280
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Answer: A: limma p-value calculated how?
... Hello Kripa, Limma uses a moderatet t-test. If you are interested in the details, you can read more in Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, ...
written 7.4 years ago by David Westergaard280
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Using limma to identify differentially expressed genes
... Hello, I've been trying to use limma to identify genes from the following data: http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-21340 - It's a simple control vs. disease experiment # SDRF downloaded from above page SDRF <- read.table(file="E-GEOD-21340.sdrf.txt",header=TRUE,stringsAsF act ...
limma written 7.5 years ago by David Westergaard280 • updated 7.5 years ago by Voke AO760
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Comment: C: how to map Affymetrix ID to ensemble gene ID
... Dear Shan Gao, Perhaps you can try this: >ensembl <- useMart("ensembl", data = "sscrofa_gene_ensembl") >filters <- listFilters(ensembl) Looking through filters for anything related to affymetrix yields this: > filters[grep("Affy",filters$description),] name descri ...
written 7.6 years ago by David Westergaard280
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Answer: A: how to map Affymetrix ID to ensemble gene ID
... Hello, I guess you would use the http://www.bioconductor.org/packages/release/data/annotation/html/porc ine.db.html package, you can read more about the functions in the vignette http://www.bioconductor.org/packages/release/data/annotation/manuals/p orcine.db/man/porcine.db.pdf If that doesn't sui ...
written 7.6 years ago by David Westergaard280
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Comment: C: arrayQualityMetrics error and question
... Dear Wolfgang, I have successfully updated cairo graphics library to version 1.10.2. Everything is working, but I am still getting the warnings that Daniel describe. They are of no concern, since it is working, but if you need more info to reproduce the warnings, let me know. Best, David 2012/3/8 ...
written 7.6 years ago by David Westergaard280
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Comment: C: arrayQualityMetrics error and question
... Dear Wolfgang, I think that it may be a slighty broken Cairo installed in my homedir. Sadly, our Cairo graphics installation at the institute is quite old, version 1.0. arrayQualityMetrics depends on the R package Cairo which depends on a Cairo graphics installation >= 1.2. I think I may the ins ...
written 7.6 years ago by David Westergaard280
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Comment: C: arrayQualityMetrics error and question
... Hi, It seems to be working now, with arrayQualityMetrics v3.10. The only "problem" is, I am getting alot of warnings, more than 50. All of them are: In grid.Call.graphics(L_segments, x$x0, x$y0, x$x1, x$y1, ... : X11 protocol error: BadMatch (invalid parameter attributes) Can I just disregard t ...
written 7.6 years ago by David Westergaard280

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