User: Sebastian Thieme
Sebastian Thieme • 60
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Posts by Sebastian Thieme
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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 7.9 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 7.9 years ago by
Sebastian Thieme • 60
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... 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 8.0 years ago by
Sebastian Thieme • 60
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... 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 8.0 years ago by
Sebastian Thieme • 60
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... 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 8.0 years ago by
Sebastian Thieme • 60
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... 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 ...
written 8.0 years ago by
Sebastian Thieme • 60
• updated
8.0 years ago by
James W. MacDonald ♦ 52k
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