User: David Westergaard

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Posts by David Westergaard

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Answer: A: limma design and contrast matrix for paired experiment
... Dear Gordon, Thank you for your reply. Following the example from the edgeR users guide, I revised the model: CellLine <- factor(rep(c('C1','C1','C2','C2'),3),levels=c('C1','C2')) Sample <- factor(c(1,1,2,2,3,3,4,4,5,5,6,6),levels=c(1,2,3,4,5,6)) Treatment <- factor(rep(c('C','T'),6),leve ...
written 6.2 years ago by David Westergaard280
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limma design and contrast matrix for paired experiment
... Hello, I am analysing microarray data performed on two cell cultures, in which the gene expression were measured before (C) and after treatment (T), so that the targets look like this: Cell-line Treatment Sample Cell 1 C 1 Cell 1 T 1 Cell 2 C 2 Cell 2 T 2 Ce ...
microarray written 6.2 years ago by David Westergaard280
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Answer: A: Obtaining protein sequence data?
... Hi Caitlin, If you have found the protein sequences at NCBI Protein, they are (unless otherwise specified) what you could call 'healthy'. I am not quire sure what you mean by damaged copies. You will have to investigate the litterature to see which BRCA1/2 mutations are found in breast cancer. To m ...
written 6.3 years ago by David Westergaard280
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Comment: C: Advice on experimental setup
... Hi Alex, That was a very informative reply on a difficult question, I think you very much for your advice. I might revive this mail at some point, when we get closer to the actual statistical analysis. Best, David 2012/9/6 Alex Gutteridge : > On 05.09.2012 13:53, David Westergaard wrote: > ...
written 6.5 years ago by David Westergaard280
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Comment: C: Advice on experimental setup
... Hi Alex, There is no control group as such. One of the diets is somewhat of a control group, but not quite because it is still a diet that has some 'special' properties. I am used to working with experiments which has atleast one control group, so this setup is a bit out of my domain, which is the ...
written 6.5 years ago by David Westergaard280
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Advice on experimental setup
... Pardon the spam, I forgot to include the list. Best, David 2012/9/5 David Westergaard : > Hi Sean, > > Groups 1, 2 and 3 are no different except for the diet being fed. > > Best, > David > > 2012/9/5 Sean Davis : >> >> >> On Wed, Sep 5, 2012 at 4:55 AM, Da ...
limma written 6.5 years ago by David Westergaard280 • updated 6.5 years ago by Sean Davis21k
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Advice on experimental setup
... Hello, I am assisting in the setup of an experiment, in which 3 groups, each consisting of 8 subjects, will be fed 3 diets: Group 1 - Diet A Group 2 - Diet B Group 3 - Diet C We plan on using limma to identify the differentially expressed genes. Reading the limma users guide, a factorial design ma ...
limma written 6.5 years ago by David Westergaard280 • updated 6.5 years ago by Alex Gutteridge650
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Answer: A: XML package cannot be installed
... Dear Wayne, XML is complaining it cannot find xml2-config (From Cannot find xml2-config). You need to have the libxml2 package installed on your system. If you are running a debian flavor, you can get it from aptitude. I'm not familiar with redhat, but I guess it should be in whatever packaging sy ...
written 6.7 years ago by David Westergaard280
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Answer: A: entrez gene summary
... Dear Amit, You can retrieve the XML record by making use the Entrez Programming Utilities. This is descirbed at http://www.ncbi.nlm.nih.gov/books/NBK25499/. Looking through the page, they give an example of how to retrieve the XML record for a gene: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efet ...
written 6.7 years ago by David Westergaard280
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Comment: C: Printing arrayQualityMetrics report
... Hi, I actually managed to produce a sufficient pdf to include just by upgrading my browser and fixing minor issues in inkscape. Thanks for the help, David 2012/6/22 Wolfgang Huber : > Dear James > > that is one way to go about it. A more direct way for getting at this table > is to ke ...
written 6.7 years ago by David Westergaard280

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