Displaying 20 results from an estimated 700 matches similar to: "Filters()"
2012 Jan 24
1
gsub semicolon with double quotation mark
Hi,
I would like to substitute a semicolon with two double quotation marks and
a comma inbetween.
It suppose to look like that:
I have:
FBpp0070086;FBpp0099643;FBpp0112915
I would like to have:
"FBpp0070086","FBpp0099643","FBpp0112915"
I tried with various numbers of backslashes, but noe have worked.
for example:
gsub(";", "\\\",\"",
2005 Oct 19
1
Unix proxy and firewall problems
I was trying to install R on a unix server. Because of a firewall i can't
install biocLite for working with Bioconductor.
With windows it wasn't a problem. I used the option '--internet2' to bypass the
firewall.
I don't have any idea, how to do it with unix.
I tried to set my proxy
>Sys.putenv("http_proxy"="http...:8080")
2006 Jan 31
1
changing the default repositories
Hello,
Is it possible to change the default repositories?
I've already changed the list in the repositories file under etc/
this is how my repositories file under R/etc looks like:
row name menu_name URL default source win.binary
mac.binary
CRAN CRAN @CRAN@ TRUE TRUE TRUE TRUE
BioC Bioconductor http://www.bioconductor.org TRUE TRUE
TRUE FALSE
2010 Jul 08
2
random sample from arrays
Hello R users,
I'm trying to extract random samples from a big array I have.
I have a data frame of over 40k lines and would like to produce around 50
random sample of around 200 lines each from this array.
this is the matrix
ID xxx_1c xxx__2c xxx__3c xxx__4c xxx__5T xxx__6T xxx__7T xxx__8T
yyy_1c yyy_1c _2c
1 A_512 2.150295 2.681759 2.177138 2.142790 2.115344 2.013047
2010 May 12
1
paste two columns of a matrix by rows
Hello,
I'm trying to paste two columns of a matrix
GB_ACC GENE GENE_SYMBOL
NM_010657 NM_010657
NM_027162 NM_027162
NM_198863 NM_198863
NM_010727 NM_010727
These two column are a part of a 41,000 x 26 matrix.
I wanted these two column to be pasted into one (the firstone, GB_ACC). I
tried to do it with a for loop, but it takes ages to finish:
for( i in
2010 Jun 14
2
merging data frames
Hi,
is it possible to merge two data frames while preserving the row names of
the bigger data frame?
I have two data frames which i would like to combine. While doing so I
always loose the row names. When I try to append this, I get the error
message, that I have non-unique names. This although I used unique command
on the data frame where the double inputs supposedly are
thanks for the help
2011 Oct 25
4
comparing two tables
Hi everybody,
I would like to know whether it is possible to compare to tables for certain
parameters.
I have these two tables:
gene table
name chr start end str accession Length
gen1 4 646752 646838 + MI0005806 86
gen12 2L 243035 243141 - MI0005821 106
gen3 2L 159838 159928 + MI0005813 90
gen7 2L
2010 May 11
1
comparing and combing files
Hello,
I have two tab-delimited files which I would like to combine.
In the first one I have gene IDs (Unique) on column 1 and than various
experimental results from microarray analysis (see attached files list1 )
the second arrays have the same genes IDs (more and in a different order,
some are double) (see attached files list2 )
What I would like to do is to search in the second list for gene
2010 Jun 10
2
adding column of ordered numbers to matrix
Hello everyone,
I have a matrix of over 40000 line and about 30 columns.
For my analysis I would like to add another column with ascending numbers
(column header should be "order", and than 1,2,3,4 ....the end of the
matrix).
During my analysis I reorder them ( due to merge commands by a different
column).
How do I add such a column in an ascending order (or descending for what it
2010 Jul 08
2
transformation of data.frame
Hello all R users,
I have a problems transforming (or maybe better regrouping) a data.frame.
I have a big data.frame, which I would like to sum up according to a
specific column.
This is an example of my matrix:
ID gen
0042787 gen2
0016070 gen2
0016070 gen3
0007409 Gen1
0007409 gen3
0006511 gen2
0006417 gen3
0016070 gen4
0006511 gen4
I want to rearrange the matrix
2011 Feb 09
1
samr - extract genes from siggenes.table
Hi BioC user,
I have a problem extracting the gene set I would like to work with.
Here is I work with my data:
normData <- read.delim("normalizedData.txt",sep ="\t")
######### two class unpaired comparison
# y must take values 1,2
classes <- c(-1,-2,1,2)
#prepere the data for the samr analysis
data.x <-as.matrix(normData[,8:11])
d=list(x=data.x,y=classes,
2008 Oct 09
1
R loops
hello everybody,
I have a directory with over 3000 files with different names. I would like
to make some vectors with the file names which are belong together.
I'm trying to do it with a for loop in R:
SF <- c("ad", "cd", "cer", "stress", "salty", "PC", "high", "transfer",
"cold",
2010 Feb 08
1
objects masked from packages
dear all,
I have a problem with a masked object in a package we created here.
we make a package for a workflow of internal analysis of microarray data.
to create the package we used:
> install.packages(pkgs="affyAnalysis", repos=NULL)
> R CMD INSTALL affyAnalysis
Erzeuge Verzeichnisse ...
Erzeuge DESCRIPTION ...
Erzeuge NAMESPACE ...
Erzeuge Read-and-delete-me ...
Kopiere
2010 May 10
1
Rd files must have a non-empty \title
Hello everybody,
I'm trying to install a package I have built. This package contains three
scripts with various functions (S3 as well as S4 classes)
I run at first the package.skeleton command with:
> package.skeleton("affyAnalysis", namespace=TRUE, code_files =c("defS3.R",
"defS4.R", "qc.R"))
affyAnalysis is the name of the supposed package and
2008 Oct 10
0
Antwort: FW: R loops
it did help to create the separate vectors. The problem is, I would like
to continue working with each vector on its own and make some further
analysis.
For that i need to allocate each vector in the filePatterns a unique name,
which I just can't do.
I'm not so great in R loops and the help over the net regards for loops in
R is quite rare.
I'm really thankful for every help.
2008 Jan 22
3
gctorture and proc.time (PR#10600)
In R version 2.6.1 (2007-11-26)
and R version 2.6.1 Patched (2008-01-19 r44061)
on openSUSE 10.2 (X86-64)
> gctorture()
> proc.time()
Error: protect(): protection stack overflow
The problem with this is that then
R CMD check --use-gct foo
ALWAYS FAILS with
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
Error in
2011 Mar 26
1
core Matrix package segfaulted on R CMD check --use-gct
Current core/Recommended Matrix package (0.999375-48) has been segfaulting against R 2.13-alpha/2.14-trunk for the last week or so (since R-2.13 was branched, when I started trying) when "run with R CMD check --use-gct":
--------------
> pkgname <- "Matrix"
> source(file.path(R.home("share"), "R", "examples-header.R"))
>
2011 Nov 18
2
libpng warning: Application built with libpng-1.2.26 but running with 1.5.2
Hi,
I have a problem on my mac when trying in R to produce png images.
I am getting this warnings with the ArrayQualityMetrics package:
> arrayQualityMetrics(rma_fatBody, outdir="normData", force =T)
The report will be written into directory 'normData'.
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
(loaded the KernSmooth namespace)
libpng warning: Application built
2011 Oct 15
2
gctorture() and gzfile() doesn't get along.
Found the simpliest way of seeing I bug I encountered doing "R CMD check --use-gct": Just launch R (with --vanilla), and do this:
> ?gctorture
# this work
> gctorture()
> ?gctorture
Error in gzfile(file, "rb") :
can only weakly reference/finalize reference objects
# this does not
It seems that when gctorture() is on gzfile() doesn't work.
2012 Jan 11
3
Command completion of the R binary / Ubuntu
Dear Deepayan and dear list,
I notice a small inconsistency with the command completion of the R CMD
check. --no-latex is deprecated sincs R 2.12.0 and defunct since 2.13.0
but the command line completion still suggests it:
cb at cbdesktop:~/r-devel$ bin/R CMD check --no-<here I hit tab>
--no-clean --no-examples --no-latex --no-vignettes
--no-codoc --no-install