User: Sebastian Thieme

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Posts by Sebastian Thieme

<prev • 6 results • page 1 of 1 • next >
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Comment: C: biomart to a data.frame
... Hi Assa, you can try this con <- textConnection(data2seperate) seperatedData <- read.table(con,sep=";",stringsAsFactors=FALSE) #splitten It's nearly the same as the strsplit function but you get a table as output sorted by your input. I hope this helps. Best Basti 2012/1/26 Assa Yerosla ...
written 6.2 years ago by Sebastian Thieme • 60
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Comment: C: how to set R memory limit
... Hello, I had such a problem several times ago. Look at the option() parameter there you can set the RAM limit. e.g. options(java.parameters = "-Xmx8192m") to allocate 8GB RAM. the default is 1024MB I think. Best regards Basti 2012/1/10 Steve Lianoglou : > Hi, > > On Mon, Jan 9, 2012 at ...
written 6.3 years ago by Sebastian Thieme • 60
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Answer: A: Problems selecting rows from dataframe (exprs) of GNF Atlas data....
... Hi Bas, the numbers are not the rownames. if you use rownames(exprs) you get a list of the names your rows have so the numbers are only the position within the list. If you do something like exprs <- as.data.frame(exprs(eset)) x <- rownames(exprs) exprs[x %in% x,] you should get the entire d ...
written 6.3 years ago by Sebastian Thieme • 60
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Answer: A: Problems selecting rows from dataframe (exprs) of GNF Atlas data....
... Hello, happy new year too =) you can use exprs[ rownames(exprs) %in% "gnf1h00499_at",] or exprs[ rownames(exprs) %in% vectorOfNames,], where vectorOfNames is a list or a vector of the names you are looking for. Important is that the object you are search in has to be the first argument. If you wan ...
written 6.3 years ago by Sebastian Thieme • 60
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Answer: A: biomaRt access to ensemble genomes 11 fungi_mart_11
... Hi Malcolm, I have a older version of biomaRt 2.6.0 but I think it doesn't matter. If you make library("biomaRt") listMarts() you get all available marts if your mart is not listed it is not available right now. In my version is only fungi_mart_10 ( ENSEMBL FUNGI VARIATION 10 (EBI UK)) available. ...
written 6.3 years ago by Sebastian Thieme • 60
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problems with pd.genomewidesnp.6
... Hi at all, I have some problems with the pd.genomewidesnp.6 package and I hope some one can help me. The info with get(objects("package:pd.genomewidesnp.6")) is #Class........: AffySNPCNVPDInfo #Manufacturer.: Affymetrix #Genome Build.: HG19 #Chip Geometry: 2572 rows x 2680 columns I want match ...
process written 6.3 years ago by Sebastian Thieme • 60 • updated 6.3 years ago by James W. MacDonald ♦ 46k

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