that worked, but the entire set of 25,000 probes didn't
work, then you may have some incorrect probe names that are causing
the error. Try cutting the list in half and seeing if one half works
but the other half doesn't. If there...are a few incorrect probe names,
it may take some sequential halving of the list to find them.
2) I don't think you can call RemoveProbes() more than once without...O…
Order by: Relevance
<div class="preformatted">
Hello,
I am trying to read and work with data from an Affymetrix tiling
array.
(And appreciate the previous posts for working with such data)! I am
using the packages "makePlatformDesign" and "oligo".
I have successfully used the makePDpackage function to create the
needed
package (pd.at35b.mr.v04.2.tigrv5)
makePDpackage("At35b_MR_v04-2
_TIGRv5.bpmap", type="…
dds$Condition <- factor(dds$Condition, levels = c("Normal","Tumor"))
res <- results(dds, name="Condition_Tumor_vs_Normal", alpha=0.05, lfcThreshold=0.58)
resOrdered <- res[order(res$pvalue), ]
```
```r
> summary(res)
out of...NA
A2ML1 5.00733 0.0147204 1.32641 0 1 NA
```
All genes are named in this range: A1CF --> A2M…
Hi,
I?m using the package RODBC to read data from MS Excel.
In the (special) case of Excel sheet?names containing a space
character
(eg ?Feuil 1?), I?m having trouble to access the data in such sheets.
Similarly, defining a "print...area" in Excel (from a sheet without " "
in
it's name) will give an additional line in sqlTables that is of
table_type "TABLE", but I can't read it neither. A clos…
updated 19.0 years ago • Wolfgang Raffelsberger
function:
Reading in .RCC files......
Checking codeset contents......
Checked gene name consistency in .RCC files.
Fehler in dat[[1]] : Indizierung außerhalb der Grenzen
I tried to use a zip file format with RCC files...and I also tried to use my uploaded vector.
Please find the r-code below.
Do you have an advice for me?
Best regards,
Anna
#loading_meta_data
```r
CME_Sample_data <..…
updated 18 months ago • anna.kuntze
nbsp;
__How to apply:__
Applications, including a CV and a Reasons for Applying statement (2,500 character limit), must be made via the University of Cambridge Graduate Admissions website. Applicants must select up
updated 7.1 years ago • Shamith.Samarajiwa
guess, and that's all I can do given the
information you've provided, I'd say look at the parameter names in
your flowFrames. Sometimes R will substitute a '.' for the '-'
character in parameter names.
Greg Finak, Ph.D
Post-doctoral...V450-A APC-A Alexa 700-A QDot 655-A APC-Cy7-A Pac Orange-A
>
> The following are the column names of each flowFrame:
> FSC-A FSC-H SSC-A SSC-…
encounter the problems as following:
combine2.3<-merge(combine2.1,TALL)
Error: cannot allocate vector of size 409600 Kb
Question2:
Affybatch BCR does not have names for each sample (only H).
> > > setwd("/export/home/fwan/data
lt;- matrix(charToRaw(as.character(unlist(qual))),
nrow=length(qual), byrow=TRUE)
Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
negative length vectors are not allowed
Calls: trimRead ... matrix -> charToRaw -> unlist -> unlist -> .Call2
updated 13.8 years ago • wang peter
read.csv("data.csv")
nSets = 1
setLabels = c("alpha")
shortLabels = c("alpha")
multiExpr = vector(mode = "list", length = nSets)
multiExpr[[1]] = list(data = as.data.frame(t(alphaData[-c(1:8)])));
names(multiExpr[[1]]$data) = alphaData$substanceBXH...rownames(multiExpr[[1]]$data) = names(alphaData)[-c(1:8)];
exprSize = checkSets(multiExpr)
exprSize
gsg = goodSamplesGenesMS(multiExpr, ver…
updated 10.0 years ago • sm15766
with DESeq2?
I can run `` DESeq:: ```` estimateDispersions(...) ``but that produces two dispersion vectors. How I'm not sure how to integrate these dispersion vectors into DESeq2. It seems like there is only room from one dispersion...vector in the analysis.
Ben
updated 9.2 years ago • bkellman
with 6 rows and 2 columns
type description
<character> <character>
baseMean intermediate the base mean over all rows
log2FoldChange results log2 fold change (MAP): condition...34 972 336 101
fax: +34 972 337 806
www.ceab.csic.es
[[alternative HTML version deleted]]
</character&g…
of said issue. Please see R response and session info further below.
<pre>
BED_TEXT <- "track name=\"My track\" description=\"My description\" visibility=2 itemRgb=\"On\"
chr1 567890 567899 DAT:0.1234 0 . 0 0 255,0,0"
BED_FILE <- "test.bed...tryCatch(
import(con = BED_FILE, format = "bed", trackLine = TRUE, genome = "hg19", extraCols = "character"),
error = function(…
updated 7.8 years ago • cbaribault
the AnnotationDbi package but I get an error. It says that two fields in the source DB have the same name. The same error raises when trying to get the keys for "GO" and "EVIDENCE".
Could you please help me to solve this issue? Thank...to GO mapping data...
Error in FUN(X[[i]], ...) :
Two fields in the source DB have the same name.
> sessionInfo()
R version 3.6.3 (2020-02-29)
Pl…
updated 5.6 years ago • jdiaz
from a affy experiment). I have 10 normals and
15 cancer lines.
of 180 I have some duplicate gene names (arising from
two different probesets for a single gene).
I want to calculate the median expression value for
these two
updated 17.8 years ago • Srinivas Iyyer
Dear all,
I have used CopywriteR package with sequencing data and got an error.
Because I previously got a successful result with a different set of bam files, I think the problem would be the bam list (or some of the bam files), but I don't figure out what exactly is the problem.
My script, error messages and sessionInfo() are attached below.
Script:
<pre>
library(CopywriteR)
BAMl…
updated 9.5 years ago • Tom
lt;-cbind(rep(1,12),rep(c(pd$Sample_Group)))
#3 groups of 4 samples each, pd from pData in minfi
#naming y from the vignette as data
#naming X from the vignette as layout
tab <- bumphunter(data, layout, chr, pos, clust, cutoff=.5...Error in S %*% vv : requires numeric/complex matrix/vector arguments
Any help would be much appreciated.
-- output of sessionInfo():
> sessionInfo()
…
updated 12.5 years ago • Guest User
<div class="preformatted">Hi All,
For a while I have been using these lines below to normalize a large
Affy
data set with customCDFs and gcrma. I can't seem to make it work
anymore.
For some reason, in the affinity adjustment of gcrma, there is a
switch to
the affy CDF which gives an error later. Its a bit puzzling. I am
confident
the cdf name is correct and I even updated the custom CDFs …
none")
When I output this table I have all the statistical data as expected
but not
the gene names and annotation,etc that the help file says should also
be
included.
I guess I must have missed out a step but I'm not sure
updated 19.9 years ago • Quentin Anstee
I have a custom annotation package which I created using
"AnnBuilder"
package. The package named "ipihs324" has annotation for IPI
identifiers
and contains mappings to Entrez ids in the environment variable
ipihs324ENTREZID...Error in mget("IPI00000948", env, ifnotfound = list("FALSE")) :
second argument must be an environment
##########################
As I want to write a generic code for lo…
updated 18.1 years ago • Chanchal Kumar
External("dotTcl", ..., PACKAGE = "tcltk"), class
=
"tclObj") :
[tcl] ambiguous option "-col": must be -column, -columnspan,
-in, -ipadx, -ipady, -padx, -pady, -row, -rowspan, or -sticky.
May this have anything to do with the environment...variable set up for
Tcl/Tk?
I have it as follows:
Variable name: TCL_LIBRARY
Variable value: c:\tcl\lib\tcl8.4.
Thanks again for all your suggesti…
I have received several inquiries about a recent error in FELLA.
The message, after calling **buildGraphFromKEGGREST**, looks like the following:
Error in .getUrl(url, .listParser, nameColumn = 1, valueColumn = 2) :
Not Found (HTTP 404)
This is due to our dependency KEGGREST, so we must wait for a fix on their behalf.
In the meantime, we have shared some FELLA databases f…
updated 6.2 years ago • sergi.picart
I tried this:
sapply(network_day_0, class)
Node.1 Node.2 wTO
"character" "character" "numeric"
And this:
class(network_day_0$wTO)
[1] "numeric"
I'm not able to find the mistake. Can someone please
gt; summary(a)
Length Class Mode
R.version 13 -none- list
platform 1 -none- character
locale 1 -none- character
basePkgs 7 -none- character
otherPkgs 7 -none- list
loadedOnly 23 -none- list
> summary(b)
Length...Class Mode
R.version 13 -none- list
platform 1 -none- character
locale 1 -none- character
basePkg…
updated 14.8 years ago • Guillaume Meurice
values within a heatmap plot
> labeledHeatmap(Matrix = moduleTraitCor,
+ xLabels = names(design2),
+ yLabels = names(MEs),
+ ySymbols = names(MEs),
+ colorLabels = FALSE,
+ colors = greenWhiteRed(50),
+ textMatrix = textMatrix,
+ setStdMargins...paste("Module-trait relationships…
updated 3.7 years ago • ayabalbaa1990
<div class="preformatted">Can anyone help me with this, I cannot recreate a web service on a 2nd
machine?
I've developed and tested an RWebservices based web service on CentOS
release 5.3 (Final) running in a VM on my windows XP box.
However, when I transferred the code to my production machine, CentOS
release 5.4 (Final), I cannot map the package (e.g. generate Java
code).
Other differ…
updated 16.0 years ago • Michael P Shipway
Cancer data set consists of 40 cancer samples and 40 matched healthy controls. I defined the class vectors and origin vectors accordingly:
#class vector
n1 <- 40
n2 <- 40
cl <- rep(c(0,1), c(n1,n2))
# origin vector
origin <- rep(1, n1+n2)
#rankprod...than 60 samples (30 cancer + 30 healthy controls), I receive an error message that reads: "Error:…
interest (there are 62 of them). What should I write to make such a table (where should I place the names of the genes)? My code at the moment:
Code should be placed in three backticks as shown below
```
gset <- getGEO("GSE24742", GSEMatrix...TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[…
updated 3.0 years ago • Элина
str(eset)
Error in readExpressionSet(exprsFile, phenoDataFile, header = TRUE,
sep
= "\t") :
Column names of expression matrix must be identical to
the sample names of the phenodata table.
You could use 'options(error=recover
updated 17.5 years ago • daphne mouzaki RI
Dear community,
I have encountered a problem when trying to import the data using tximport
From what I know about the data, it is obtained through RSEM technology, but the columns are a little different from what I read in the forum. First of all, I have 100 files of *.gene.fpkm.csv and another 100 of *.transcript.fpkm.csv "nature", which from the beginning are rather different from the tximp…
Hello,
I am trying to extract the genomic coordinates (chromosome name, start position, end position) from an MIndex object but can't figure out how to do it.
Can someone help?
Here is the code - first...Hello,
I am trying to extract the genomic coordinates (chromosome name, start position, end position) from an MIndex object but can't figure out how to do it.
Can someone help?
Here is the …
I'm wrestling with tximport/DESeq2. I've create a small experiment dataset of 2 paired end fastq, generated counts with salmon, and successfully read them in with tximport (or so I think). "files" is my list of 2 quant.sf files. tx2gene is the obvious.
> txi <- tximport(files, type = "salmon", tx2gene = tx2gene)
> sampleTable
tissue
sampl…
DESCRIPTION' ... OK
* this is package 'Illumina8vprerelease.db' version '1.0.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking for executable...can be installed
... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... …
updated 15.9 years ago • John Lande
genes.fpkm_tracking
Checking samples table...
Populating samples table...
Error: Column name mismatch.
In addition: There were 50 or more warnings (use warnings() to see the first 50)</pre>
This is my session info:
<pre>
R version
updated 8.5 years ago • tannerndrsn4
integer', sep = ",", quote = 'NULL', comment.char = "")
Read 26042606 items
> class(temp)
[1] "character"
> typeof(temp)
[1] "character"
I'm new to R, and I apologize if the mistake is obvious, but could
someone explain to me why
updated 15.4 years ago • Gaston Fiore
<div class="preformatted">
This is not a question, but an information that may be useful to
everybody having problems with Rgraphviz similar to the one described
in this post.
I succeeded in solving the problem in installing Graphviz in a
directory such as its path does not include any blank character.
Everything worked well as soon as I installed Graphviz in the
following directory "C:\G…
argument
In addition: Warning messages:
1: In object$printer :
? $ operator is invalid for atomic vectors, returning NULL
2: In object$M : $ operator is invalid for atomic vectors, returning
NULL
3: In object$A : $ operator is invalid...for atomic vectors, returning
NULL
4: In object$M : $ operator is invalid for atomic vectors, returning
NULL
5: In object$A : $ operator is invalid...for atomic v…
RangedData with 4 rows and 0 value columns across 3 spaces
space ranges |
<character> <iranges> |
1 chr1 [108503809, 108508915] |
2 chr17 [ 60212870, 60218774] |
3 chr8 [ 86373507, 86380637] |
4 chr8 [ 99303547, 99307608...RangedData with 5 rows and 0 value columns across 3 spaces
space ranges |
<…
updated 14.4 years ago • Nathan Sheffield
genes,
>>>
>>> now the problem is that how can i convert the probe ID's to Gene
names
>>> using annotation package and with what database because there is
no
>>> database in bioconductor related...to t. gondii.
>>>
>>> if i have to pick these gene names from NCBI then how …
updated 15.0 years ago • Paul Geeleher
are trying to do this (the value of 'gen'). I also
have no idea how you came up with the 'track.name' vector.
In general, Gviz is using rtracklayer::tableNames to figure out which
tables and tracks are available. So you should...t understand because I have checked with the package
rtracklayer, whose your package inherits, the name of tracks and
tables. Could you help me ?
Regards
Tiph
R Command…
help,
Francesco
> novel.data<-as.data.frame(novel.snps)
> novel.data<-cbind(novel.data,name=row.names(novel.data))
> head(novel.data)
seqnames start end width strand ALT
name
chr22:17468875 chr22 17468875 17468875...gt; targetTrack <- with(novel.data,
+
GRangesForUCSCGenome("hg19",seqnames,targetRanges,strand,name))
> ses…
updated 13.9 years ago • Lescai, Francesco
list is defined so
## that I can refer to it later.
"Draw",
fields = list(hourStr = "character",
data = "numeric"),
methods = list(
getModel = function(){
return("Draw Distro")
},
getName = function(){
return(hourStr)
},
#'
#' @param strName...lt;- data[indSelect]
return(compon…
updated 3.9 years ago • johnston_Kyle
histogram plot and a cross coverage plot, after which it errors out with this error:
```
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
In addition: Warning message
updated 6.0 years ago • nikhil.ashok.joshi
<div class="preformatted">Dear all,
I am trying to package up some microarray data analysis code into a
bioconductor package and, naturally, I want to define some new generic
functions using the methods library. I have not been able to get my
package
to pass rcmd check. In particular, generic functions which I have
defined
are not recognized when rcmd check tries out the examples. Howeve…
updated 22.9 years ago • Gordon Smyth
seqnames ranges strand | tx_id tx_name
<rle> <iranges> <rle> | <integer> <character>
[1] chrM [3952, 4338] + | 122 Q0010
[2] chrM [4254, 4415] + | 123 Q0017
$Q0032
GRanges with 1 range and 2 elementMetadata values
seqnames...ranges strand | tx_id tx_name
<rle> <iranges> <…
updated 14.7 years ago • zhenjiang xu
defined differently in terms of classes (see
showMethods
below):
>
> for
>
> pattern="character", subject="character"
Hi Alex --
here 'character' could be anything -- 'the quick brown fox', whereas
>
> vs.
>
> pattern="DNAString...gt;
> ?
>
> It generates the same outcomes for the case of
>
>
&…
<div class="preformatted">Hi,
I am analizing a set of microarrays with SAM strategy using SIGGENES
package. The microarray data is the following:
Name Description
FLAG <- 7 arrays of an IP over RNA from a transgenic animal with a TAG
in
the protein of interest for the IP
Wt...a set of microarrays with SAM strategy using SIGGENES
package. The microarray data is the following:
Name…
updated 13.1 years ago • Marco Ortiz
out = "plot")
Error in lohSpec\_qual(x, y, genome) :
Did not detect required column names in x, required columns are: chromosome position n\_vaf t\_vaf sample
My lohspec file has the following columns...plotLayer = NULL, method = "slide", out = "plot")
Error: $ operator is invalid for atomic vectors
Thank you for your help i…
functions, 2 errors, 0 failures
ERROR in test_AtomicList_general: Error in match.arg(method) : 'arg' must be of length 1
ERROR in test_AtomicList_numerical: Error in match.arg(method) : 'arg' must be of length 1
VariantAnnotation...80 test functions, 1 error, 0 failures
ERROR in test_VRanges_vcf: Error in match.arg(method) : 'arg' must be of length 1</pre>
Any suggestions on how to t…
updated 8.2 years ago • ginggs
<div class="preformatted">
On 2/28/10 7:16 PM, "Tony Chiang" <tchiang at="" fhcrc.org=""> wrote:
> Hi Steffen et al,
>
> Quick question about a search query via biomaRt. Here is the code
that I am
> using:
>
> *****
> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> filters = listFilte…
updated 15.9 years ago • Hotz, Hans-Rudolf
some of the 'metadata' is lost after subsetting, e.g. the `` featureType() `` info. Also the sample names (column names) are lost...
Since I am rerunning an analysis, I know this did NOT occur in the previous versions (1.26.0 and 1.24.0...An object of class "qPCRset"
Size: 384 features, 6 samples
Feature types:
Feature names: Gene1 Gene2 Gene3 ...
Feature classes: …
updated 8.9 years ago • Guido Hooiveld
not allowed
non-unique values when setting 'row.names':
But I know for sure that my row names are unique! Any advice would be appreciated. Thanx.
carol
I use the library`` EnsDb.Mmusculus.v79 ``. However, I am somehow not able to retrieve the gene name (description). Based on the retrievable annotation info, I assumed this would be accessible through the argument`` columns
updated 8.4 years ago • Guido Hooiveld
Error in as.list.default(data.source) :
no method for coercing this S4 class to a vector
> 
updated 10.3 years ago • schasse
Verocounts)
head(d1)
dim(d1) #27556 x 6
#get the exon lengths from the annotation to input as vector for TPM calculation
txdb <- makeTxDbFromGFF(gtf, format="gtf")
exonic <- exonsBy(txdb, by="gene")
red.exonic <- reduce(exonic...prior.count=0)
VeroTPM <- data.frame(VeroTPM)
#Add in the gene names from annotation
# Find matching rows based on row names
matching_rows…
updated 2.3 years ago • gingergeiger22
in read.table(probe2ORF, sep = "\t", header = FALSE, strip.white
= TRUE) :
argument 'file' must be a character string or connection
In addition: Warning message:
the condition has length > 1 and only the first element
updated 20.9 years ago • Jacob Michaelson
In read.table(file = file, header = header, sep = sep, quote = quote, :
not all columns named in 'colClasses' exist
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu
updated 9.6 years ago • alexvpickering
samples, columns are variables
+ ## if simplify=TRUE, use only the most detailed level of taxa names in the final object
+ ## metaphlanToPhyloseq("~/Downloads/metaphlan_bugs_list")
+ .getMetaphlanTree <- function(removeGCF...tip.label <- sub("\|GCF_[0-9]+$", "", tree$tip.label)
Error: '\|' is an unrecognized escape in character string starting ""\|"
> if(simpli…
updated 4.5 years ago • Saraswati
done
Processing flanking windows in Chr4
<strong>Error in FUN(X[[i]], ...) :
assay rownames() must be NULL or equal rowData rownames() / rowRanges names()</strong></em></pre>
 
value)))){ # The columns I
don't want overwritten/removed all begin with "pos"
stop("Column names of user-specified 'mcols' must not begin with
'pos'")
}
GenomicRanges:::clone(x, rowData = local({
r <- rowData(x)
mcols(r) <- cbind(mcols
updated 11.8 years ago • Peter Hickey
Recent ...
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Answer: Guitar R package requires update due to dependency GenomicFeatures
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