User: Peter

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Peter170
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Posts by Peter

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Comment: C: error creating new exprSet
... Martin Morgan wrote: > The change is in the Biobase package, which affy et al rely > on. Biobase now checks to make sure the objects it creates are valid, > in this case that the number of exprs columns (i.e., samples) equals > the number of pData rows. > > When you say > >&g ...
written 13.5 years ago by Peter170
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Answer: A: GEOquery and platforms splitting
... Bosotti, Roberta [Nervianoms] wrote: > Hi all, > > I downloaded a GSE file from GEO using GEOquery. The GSM file contain > two "platforms": GPL96 and GPL97. I need to make two separate exprset > from the two (the GSMs are not contiguous for the two platforms, but > are mixed). Do y ...
written 13.6 years ago by Peter170
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Answer: A: Error with GEOquery
... Sharon wrote: > And, another related question is: How can I use *getGEO() * with the > already downloaded GSE2718.soft.gz file (to avoid subsequent > downlaoding). Use the filename argument to getGEO to parse and existing file, rather than downloading it again. For example: library(Biob ...
written 13.7 years ago by Peter170
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Comment: C: extracting interactions between members of the KEGG pathways
... Peter (BioConductor List) wrote: >> Hello, >> >> I was wondering whether there is an infrastructure in one of the BioC >> packages to extract connections between members of the KEGG pathways. As >> far as I can tell KEGG package allows to get the identifiers of the > ...
written 13.8 years ago by Peter170
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Comment: C: extracting interactions between members of the KEGG pathways
... > Hello, > > I was wondering whether there is an infrastructure in one of the BioC > packages to extract connections between members of the KEGG pathways. As > far as I can tell KEGG package allows to get the identifiers of the > members very easily, however I do not see a way of g ...
written 13.8 years ago by Peter170
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Answer: A: .EXP files
... LUIS F MENEZES wrote: > Hi, > I am trying to work with GEO dataset GSE2180, containing time-series experiments including 10 time points for 4 > different genotypes. The files include the .CEL and .EXP, these last ones containing the experimental information > (genotype and time point). H ...
written 13.8 years ago by Peter170
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Comment: C: Fine tuning heatmap.2 graphics
... > BTW, what is the advantage of heatmap2() over heatmap()? heatmap.2 can show a color key (use key=True) and density information histograms. The color key is probably not so important if you are letting the heatmap function scale your data - see also option scale="none" > Does anyone know o ...
written 13.8 years ago by Peter170
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Answer: A: Explaining limma, design matrices and linear models to non statisticians
... Natalie P. Thorne wrote: > As promised, I have put the ppt slides I have for explaining design > matrices on the web for download. Thank you for sharing them. I just had look using MS PowerPoint 2002 SP3, and found lots of the text seems to be badly positioned. I think this is a font prob ...
written 13.8 years ago by Peter170
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Comment: C: Drawing network graphs (i.e. nodes and edges)
... Peter wrote: >> Does anyone know of any existing R (r-project) code/library/package >> for drawing graphs - the network variety consisting of nodes and >> edges (or points and lines/arrows)? >> >> e.g. Genes and interactions Sean Davis wrote: > Look at Rgraphvi ...
written 13.9 years ago by Peter170
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Drawing network graphs (i.e. nodes and edges)
... Does anyone know of any existing R (r-project) code/library/package for drawing graphs - the network variety consisting of nodes and edges (or points and lines/arrows)? e.g. Genes and interactions For example, I might have a list of three edges for four genes: Gene1 -> Gene2 Gene2 -> Gene3 ...
network written 13.9 years ago by Peter170 • updated 13.9 years ago by Saurin D. Jani360

Latest awards to Peter

Popular Question 13.5 years ago, created a question with more than 1,000 views. For GEOquery and different types of GPL annotation files

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