ignore.case=TRUE), 'dataset' ]
</pre>
__`` list ``__ clearly shows a data.frame containing character strings, __`` is.character( dataset.name) ``__ is __`` TRUE ``__,<code><strong> </strong></code>__`` dataset.name == "hsapiens_gene_ensembl...pre>
set <- useDataset(dataset.name, mart=mart)</pre>
gives
<pre>
Error in (function (cl, name, va…
Order by: Relevance
x) usage.
The on-line documentation reads:
"For CharacterToFASTArecords, the (possibly named) character vector to
be converted to a list of FASTA records as one returned by readFASTA"
Since I have description and
updated 16.5 years ago • mauede@alice.it
of the columns in the beta matrix will affect the cpg sites finally found. When I matched the column names of the beta matrix identical with the row names of the PD files, I even got the 'Error: ChAMP.DMP Have not detected even one...Section 1: Check Input Pheno Start ]
You pheno is character type.
Your pheno information contains following groups. >>
<1>…
updated 4.4 years ago • Jinyue
<div class="preformatted">Hi,
here is another little possible glitch with RangedData and cbind(),
actually would like to propose to
change or expand the behavior of the cbind function or to add to it's
documentation. The use-case is as
follows:
Assume we have some chromosomal Ranges in a RangedData object. Then we
can iteratively compute statistics on
these ranges and attach them to the Da…
updated 15.8 years ago • Michael Dondrup
Secondly, when i use the reportHTML on my mQC file, the following error appears
> Error in names(miss.df) <- c("x", "y") :
'names' attribute [2] must be the same length as the vector [1]
Looking into the names, there is an obvious difference
updated 6.1 years ago • laural710
FALSE, stringsAsFactors=FALSE)
> rn<-paste(data[,1], sep="")
> P_values=data[,-1]
> names(P_values)<-rn
> myGOdata=P_values
> relevant.genes <- factor(as.integer(all.genes %in% myGOdata)
+ )
> names(relevant.genes...There are no adj nodes for node: GO:1905313
Error in switch(type, isa = 0, partof = 1, -1) :
EXPR must be a le…
updated 8.9 years ago • hollinew
conds, normalization = "none")</pre>
`` nc ``is a 14543 x 16 dataframe containing genes as row names and library names as column names. Each column of the dataframe is a numeric vector.
`` conds `` is a character vector of length...16 that is identical to the names of the column in the data frame. Some names are duplicated which indicates replicate libraries.
The error I get upon running
updated 9.2 years ago • snamjoshi87
aln <- readAligned(dirPath=dir,type="MAQMap")
Error: UserArgumentMismatch
'dirPath', 'pattern' must be 'character(1)'
I tried specifying the pattern argument but the function still doesn't
work.
> aln <- readAligned(dirPath...dir,pattern="S.*",type="MAQMap")
Error: UserArgumentMismatch
'dirPath', 'pattern' must be 'character(1)'
Is this a bug or am I doing something wr…
with between group analysis (BGA) from the made4 package
and I have a problem with some of the affy names:
I tried
bga.suppl(training.set[list,], supdata=test.set[list,],
classvec=cl_train, supvec=cl_test)
'training.set' and 'test.set...are expression sets, and 'cl_train' and
'cl_test' the corresponding classification vectors.
'list' contains some selected affy IDs.
>list
[1] "217367_s…
updated 19.1 years ago • Heike Pospisil
value where TRUE/FALSE needed
a.target <- read.marrayInfo("E-MTAB-109.sdrf.txt")
> Error in names(x) <- value :
> 'names' attribute [30] must be the same length as the vector [7]
--
Sent via the guest posting facility at bioconductor.org
updated 13.8 years ago • Guest User
s design model. I was given samples coming from : 2 cell lines, grown in 2 medias, with 2 different vectors. Is there a way to capture all of the interactions? For example:
Base differences between cell lines
Base differences...within cell line, between medias.
Base differences within cell line, within medias, between vectors.
I've tried a couple of different strategies, but am getting a…
updated 7.0 years ago • jbard
eg.: 3; 5; 8; etc.). Please, note the output bellow:
Best solution value 22681.46
Decision vector 17 29 5 48 51 37 49 4 16 40 9 44 8 6 3 3 13 28 22 19 12 30 32 41 46 23 21 38 50 11 25 26 38 44 31 15 45 49 36 43 20 34 39 33 43 8 23 35 5 48 10 18...Thus, I would like to ask wich parameter i have to use to avoid repetition in my decision
Vector
updated 6.7 years ago • jullianesantos1995
details:
call: match.arg(synchronous, c("off", "normal", "full"))
error: 'arg' must be NULL or a character vector
Error: loading failed
Execution halted
ERROR: loading failed
\* removing ‘/home/gerald/R/x86
updated 11.0 years ago • g_bothe
Hello everyone,
I have a problem with creating OMICS object in my analysis.
After downloading a TCGA data for glioblastoma I have tried crating OMICS object but unfortunately I stumbled upon a problem.
Downloaded data from TCGA includes access number and not symbol of the gene.
```r
library(pathwayPCA)
library(TCGAbiolinks)
library(tidyverse)
library(SummarizedExperiment)
query…
updated 3.1 years ago • Mikołaj Mierzejewski
I'm getting this error when I run the hyperGTest function (GOstats package) for one list of gene IDs that I'm interested in.
<pre>
Error in order(pvals) : argument 1 is not a vector</pre>
I have already checked the file and the list itself but I haven't been able to solve the problem, since it only happens for this specific list of genes when I have been able to run the test on oth…
updated 9.5 years ago • sarajdcardoso
DMRcate package). However, I keep getting this error:
Error in .local(GdObject, ...) :
'groups' must be a vector of similar length as the number of rows in the data matrix (19)
```
GRset <- preprocessFunnorm(methylset)
betavals...lt;- data.matrix(betavals)
disease <- c(UlcerativeColitis="magenta", Normal="forestgreen")
names(disease) <- levels(factor(met_annot$Chara…
updated 5.1 years ago • Julie
Dear list
I'm trying to do a rank porducts analysis on an expression set and I
cannot get the gene names onto the results table. The error is
'gene.names should have the same length as the gene vector' but I'm
giving topGene column...0 of the data matrix I gave RP so how can they
have different lengths? What exactly is the 'gene vector' mentioned
in the error?
My working below.
Many thanks fo…
updated 15.6 years ago • John Coulthard
hi,
i have a little problem with my *.Rd files i write. i have to use very
often the special character "_" and in building the help files it is
no
problem, but when compiling the manual with latex it does not work. so
i replaced
updated 20.7 years ago • Dipl.-Ing. Johannes Rainer
2,4), c(3,5), 6, 5, 6, NULL)
> edgelength <- list(c(0,1), c(0,2), 3, 0, 0, "NA")
>
> edL=vector("list", length=(length(y)))
> names(edL)=y
> for(l in 1:(length(y)))
+ {edL[[l]]=list(edges=rel[[l]], weights=edgelength[[l]])}
>
> mygraph=new("graphNEL...gt; edges(mygraph)
$`1`
[1] "2" "4"
$`2`
[1] "3" "5"
$`3`
[1] "6"
$`4`
[1] "5"
$`5`
[1]…
Cuffdiff fork
cuff.res=read.delim(file="/home/user/gene_exp.diff", sep="\t")
#notice the column name special character changes. The column used to be
#cuff.res$log2.fold_change. for older versions of Cufflinks.
cuff.fc...gnames=cuff.res$gene
sel=gnames!="-"
gnames=as.character(gnames[sel])
cuff.fc=cuff.fc[sel]
names(cuff.fc)=gnames
<strong>Error in names(cuff.fc) = gnames : attem…
updated 10.1 years ago • user31888
I'm using the VariantAnnotation package and I want to intersect two VCF files to find overlapping variants. What's the most efficient way to achieve this?
I can intersect the coordinates of the two VCFs with the GenomicRanges::findOverlaps function, but I still want to make sure that the ALT fields of the intersected coordinates match. As these are represented by DNAStringSetLists it's no…
updated 10.0 years ago • dr
lt;- rep(rv[[i]], numNodes(g))
+ } else {
+ if (length(rv[[i]]) != numNodes(g))
+ stop("Attribute vector must have as many elements as 'g' has
nodes.")
+ }
+ names(rv[[i]]) <- nodes(g)
+ nA[[ names(rv)[[i]] ]] <- rv[[i]]
+ }
+ nodeRenderInfo(g) <- nA
+ return(g)
+ }
> toyDrawn...Rgraphviz_doLayout", graph, as.integer(type), PACKAGE =
"Rgraphviz")
2: graphLayout(g)
3:…
computing iqlr centering*
`Error in apply(reads.clr[these.rows, ], 2, function(x) { :`
` dim(X) must have a positive length`
`Calls: aldex.clr ... aldex.clr.function -> aldex.set.mode -> iqlr.features -> apply`
*Execution...r
# "oral_table" is a data frame with samples in columns and genera in rows (with the genera names as row names)
ALDEx2_object = aldex.clr(oral_tabl…
updated 3.0 years ago • cwarden45
Error in map_x_colnames_to_object_colnames(colnames(object)) :
the DataFrame objects to rbind must have the same colnames
```
What other column names could be causing the error message? Perhaps the error message could be
updated 6.6 years ago • Dario Strbenac
peakset!
If I directly use
dba.plotVenn(KRNMWnocml,KRNMWnocml$masks$consensus)
>Error in names(x) <- value :
'names' attribute [4] must be the same length as the vector [3]
If I check
KRNMWnocml$masks$consensus
>NULL
If I check
updated 4.9 years ago • ahua217
em>I am trying to do a heatmap, but I can't see what I am doing wrong. I get the error message: `x' must be a numeric matrix.</em></pre>
library(limma)
library(Biobase)
setwd("/export/work/geneSTdataset")
expr.rma <- read.table("tmp...44797,1:6\]
exprs(vv)
heatmap(exprs(vv))
Error:
<pre>
Error in heatmap(exprs(vv)) : 'x' must be a numeric matrix&…
updated 9.8 years ago • Biologist
syndrome of interested.
I have the following:
- Set of differentially expressed gene IDs = `DEGs` (character vector)
- Gene IDs for all genes detected in the study (i.e., those that are DEGs + those that are not DEGs) = `universe` (character...vector)
- Set of gene IDs associated with the syndrome of interest, filtered to only include those detected in the `universe` set...syndrome_genes` (…
updated 3.2 years ago • charles.foster
Hi,
I am trying to visualize the genes using DESeq2:: plotMA after LFC shrinkage. Since my design is bit complicated, I am using numerical vector for my contrast.
I obtained the result table using:
<pre>
res = results(dds, alpha=0.05, contrast = c(0,0,0,0,0,-1/7,-1/7,-1/7,1/3,0,-1/7,-1/7,1/3...using DESeq2:: plotMA after LFC shrinkage. Since my design is bit complicated, I am using nume…
updated 7.9 years ago • amalthomas111
are identical.
My case in point:
> d1
DataFrame with 3 rows and 4 columns
Name BigWigPlus BigWigMinus totalTags
<character> <character> <character> <numeric> C547 C547 mm9.C547.plus.bw mm9.C547.minus.bw...mm9.C549.minus.bw 14477276
> d2
DataFrame with 3 rows and 4 col…
config=config)
cmpIdMapping(config=config)
# convert to ensembl gene id - gene symbol vector
idMap <- getSymEnsUp(EnsDb = "EnsDb.Hsapiens.v86", ids = genes, idtype = "GENE_NAME")
ens_gene_id <- idMap$ens_gene_id
queryBy...lt;- list(molType="gene", idType = "ensembl_gene_id", ids = names(ens_gene_id))
res_list <- getParalogs(queryBy)
# runDrugTarget_Annot_Bioassay
up_col_id …
updated 4.3 years ago • komal.rathi
and the KEGG ID.
When I feed this to the buildGOmap function, I get the error:
*Error in names(object) <- nm :
'names' attribute [15883] must be the same length as the vector [0]*
I have been getting an error that I am unable...5 GO:0016887 PA0001
6 GO:0006260 PA0001
> Pa_GOMap <- buildGOmap(Pa_GOterms)
Error in names(object) <- nm :
'names' a…
updated 23 months ago • mello-vieira
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 16, mitochondrion, plasmid
Sample name(s): WTa WTb input1 input2
The total number of probes is: 2643812
Preprocessing Information
- Transformation: log
- Normalization...package I start to get some errors
that I pasted below:
> genome(Enrich) <- "sacCer2"
> names(Enrich) <- "chrI"
> session…
updated 16.1 years ago • Noah Dowell
Hi,
I've been using the following code in order to get gene names etc from ensembl based on a list of ensembl IDs from a sequencing experiment, and it has previously been running without...The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
I have trie…
updated 6.6 years ago • meesonnl
Owner/Desktop/Data/mydata2"), full.names=TRUE), read.FCS)
> as(frames, "flowSet")
Error in names(from) <- paste("V", seq(1, length(from)), sep = "") :
'names' attribute [2] must be the same length as the vector [0]
> sessionInfo()
R version
updated 16.9 years ago • Steve Lauriault
Hi! I am looking for precomputed fRMA vectors for the HG-U219 array. Do these already exist, or would I need to make them?
Thank you!
Sarah
dexseq_count.py"
with the
following error message:
Error in strsplit(rownames(dcounts), ":") : non-character argument
I would really appreciate any pointers that might help me correct my
code
or my input files.
Here is what...WT",
flattenedfile="./flattened_mm9.gtf")
Error in strsplit(rownames(dcounts), ":") : non-character argument
--------------------------------------
As far as I could un…
it?
Thanks a million....
> annotHuman <- read.csv("HG-U133A_2.na30.annot.csv", colClasses =
"character")
> annotMouse <- read.csv("HT_MG-430A.na30.annot.csv", colClasses =
"character")
> homologene<-read.delim('homologene.data...of argument
In addition: Warning messages:
1: In is.na(geneid) :
is.na() applied to non-(list or vector) of type 'NULL'
2:…
expression matrix) and design!
I read the below information\*\*\* on this website ( to make a keep vector and so on) and tried to follow the advice.
However when I try to make a keep vector for my own data I get this error: "Error: cannot...allocate vector of size 453.2 Mb".
Thanks
\*\*\*When you construct a design matrix with `` model.matrix ``, any …
updated 10.0 years ago • fahime.falahi
done
> 20121126 20:48:51| Locating...done
> AromaCellSequenceFile:
> Name: Hs_PromPR_v02
> Tags:
> Full name: Hs_PromPR_v02
> Pathname:
annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acs...file:
annotationData/chipTypes/Hs_PromPR_v02/Hs_PromPR_v02.acm
> AromaCellMatchScoreFile:
> Name: Hs_PromPR_v02
> T…
updated 13.1 years ago • Henrik Bengtsson
applied
to
a flowSet. I realize that to split without using the 'population'
argument all samples must have the same populations, which is not the
case here. Plotting the result of the filter shows populations 'area
1'
through...gt; nk <- split(Data(wf[['NK-']])[c(1,2,5)], filter_cv2_cd3,
population="area 3")
Error in `names<-`(`*tmp*`, value = c("rest", "area 1", "area 2",
"area 3"…
updated 14.7 years ago • Aric Gregson
to have errors when running my code, which is due to the read.flowSet command returning Error: vector::\_M\_range\_check.
The only option I found is to delete the fcs file corresponding to the faulty well, and run my loop again...fcs") \# find all FCS files
dataset<-data.frame() \#create empty data frame
loc0events<-vector() \#create vector
for (i in 1:length(fnames))&am…
updated 9.9 years ago • e.bestion
Hi,
I have a list where each list element is IntegerList, I want to coerce IntegerList object to vector. I tried of using `` as.vector `` function, but it is still not simplified as I expected. How can make this happen? Any idea?
I...Hi,
I have a list where each list element is IntegerList, I want to coerce IntegerList object to vector. I tried of using `` as.vector `` function, but it is stil…
updated 9.4 years ago • jian_liangli
Hi,
I would like to know using package GenVisR, is it possible to output the mutation frequency data from waterfall function to data by gene instead of sample by default? I had read the GenVisR package manual and tried to resolve using writeData function within GenVisR package, it creates error which I couldn't resolve. Here is the code i used:
```r
writeData(waterfall(mutationData, mainRecurC…
updated 6.3 years ago • sheneicechang
for 'GO.db', details:
call: match.arg(synchronous, c("off", "normal", "full"))
error: 'arg' must be NULL or a character vector
Error : package ‘GO.db’ could not be loaded
ERROR: lazy loading failed for package ‘topGO’
* removing
updated 10.8 years ago • vjimenez
Hi everyone,
I'm new to the pathview R package, and the whole bioinformatics, but have dissent experience with R.
I'm trying to create maps for different pathways using pathview::pathview(), and only in some of pathways (running the same code) I'm getting an error with "negative length vectors are not allowed".
For what I looked around it seems to be a problem with the dimensions of the…
x) usage.
> The on-line documentation reads:
> "For CharacterToFASTArecords, the (possibly named) character vector
> to be converted to a list of FASTA records as one returned by
> readFASTA"
> Since I have description...variables ... I do
> not know how to use it.
That function expects the description to be in the "names" attribute
of your character vec…
updated 16.5 years ago • mauede@alice.it
gt; ens_tables$entrezgene
[1] "gene_id" "entrezid"
> class(ens_tables$entrezgene)
[1] "character"
> ens_tables$entrezgene[1]
[1] "gene_id"
> ens_tables$entrezgene[[1]]
[1] "gene_id"
```
Wait. So the $entrezgene "table" is really...just a character vector? There's no table of gene_id in there?
Where are the actual gene ids?
Note that I'm not asking how to get the gene.…
updated 3.1 years ago • Ed Siefker
I try and use the importMAGEML()
function, I get this error:
Error in checkSlotAssignment(object, name, value) :
Assignment of an object of class "list" is not valid for slot
"maLabels"
in an object of class "marrayInfo"; is(value, "character...package: SJava
Warning message:
The Java machine is no longer initialized automatically. You must
explicitly load it in: f(libname, pkgname)
This email …
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org
when I do this:
micrTypeFilter
updated 6.1 years ago • salamandra
div class="preformatted">Hi,
ReadGbk (from GeneR) failed to read my Vector NTI file (.gp). I wonder
if there is a package to read the protein sequence written in such
format. Thank you.
Eric
[[alternative
updated 15.0 years ago • Eric Hu
unique positions per strand for scaffold_3
Calculating shift for scaffold_3
100Error in names(res) <- nms :
'names' attribute [4] must be the same length as the vector [2]
In addition: Warning message:
stop worker failed:
'clear_cluster
updated 7.4 years ago • gavrielmatt
But:
t2 <- RangedData(IRanges(start=c(7828367, 7828552,4121953),
end=c(7828402, 7828587, 4121988), names=c("a", "b", "c")),
space=c("Chr1", "Chr1", "Chr3"), mapq=c(1,2,1),flag=c(3,4,5))
(Here, I would like to keep the read names along with their positions
in
the...gt; rbind(t2,t2)
Error in validObject(.Object) :
invalid class "RangedData" object: the names of the ranges must
equal
the ro…
las=2)
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) :
'x' must be atomic
In addition: Warning messages:
1: In is.na(x) : is.na() applied to non-(list or vector) of type 'S4'
2: In is.na(x) : is.na() applied...to non-(list or vector) of type 'S4'
if using oligo::boxplot(celfiles.rma) and oligo::hist(celfiles.rma), everything is fine. However, I hav…
updated 8.8 years ago • Javier Pérez Florido
flow_auto_qc:
```r
>fs #fs is my flowSet object
A flowSet with 283 experiments.
column names(22): FSC-A FSC-H ... FJComp-PerCP-Cy5-5-A Time
>fs.ai<-flow_auto_qc(fs, remove_from = "FS_FM")
Quality control for the file: AAM_d7_CD19...Error: cannot allocate vector of size 856.3 Gb.'
```
Do you know if there are compatibility issues between flowJo and flowAI?
I have also…
updated 2.4 years ago • Simoluc
the "whiskers".
The
main box and whiskers themselves *appear* to be the same. I guess some
defaults must be different when defining the data as a formula or
explicitly naming the vectors... but I'm not finding an obvious note
as
div class="preformatted">Hi All,
I have two vectors of alleles stored as DNAStringSetLists. For each
element
in both lists, I need to find the length of the intersecting...as does sapply(dna.set.list,
as.character) (and then using mclapply or lapply to find intersect on
characters). Is there a fast way to do this? I have vectors ~12
million
rows long.
Vince
--
Vince Buffalo
Ross-Ibarra Lab …
updated 12.2 years ago • Vince S. Buffalo
I think I might have found a bug in rhdf5. Namely, calling the following in a session where library(rhdf5) has \*not\* been run:
\`rhdf5::h5write(donors, file = output\_file, name...sampleID")\`
(where "donors" is a character vector) gives the following error:
\`\`\`
Error in UseMethod("h5write") :
no applicable method for 'h5write' applied to...an object of class "chara…
updated 8.9 years ago • davis
<div class="preformatted">Dear Neeraj Kumar,
You cannot apply Tquantile normalization to your data, because the
Tquantile method is only appropriate for two-colour data whereas your
data
is single-channel.
The only valid methods for single-channel data are "scale","quantile"
or
"cyclicloess".
Best wishes
Gordon
------------- original message ------------
[BioC] Vector for Targest in Tqu…
updated 12.4 years ago • Gordon Smyth
gt;
2GB) in R with the function scanBam() in the Rsamtools package.
It stops saying "negative length vectors are not allowed".
I think my BAM-file is ok, because I can read it in small chunks like
reads on positive strand first, then...problem or
concerning the reason for this error (I don't really understand what a
"negative length vector" is).
Thanks in advance
Christoph
</div
analysis. I need to perform Tquantile
Normalization for different groups.For that i need to make one vector
to
define groups.
Here is my analysis.
y.q <- normalizeBetweenArrays(y, method="Tquantile",targets="*how to
make
targets...vector here??*")
> targets <- readTargets("limma_target1.txt")
> x <- read.maimages(targets, source="agilent",green.only=TRUE...C9
…
updated 10.2 years ago • neeraj rana
Recent ...
Replies
Answer: blockwiseModule crashes in the end and doesn't generate modules
by
Daniel
•
0
Queria compartir mi experiencia con [https://jugabet.cl/football/live/1][1]
. Esta seccion ofrece cobertura en vivo de futbol, con marcado…
Comment: Empty boxes in treemap plot rrvgo package
by
TikTsokaasocissalpc
•
0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis
by
adam80haynes
•
0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
•
0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
•
0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Votes
Awards
• All
Popular Question to
Gordon Smyth
53k
Popular Question to
Hervé Pagès
16k
Popular Question to
Istvan Albert
▴
50
Popular Question to
Dario Strbenac
★
1.6k
Locations
• All
United States, 14 minutes ago
The Netherlands, 58 minutes ago
Türkiye, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
India, 2 hours ago
United States, 14 minutes ago
The Netherlands, 58 minutes ago
Türkiye, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
India, 2 hours ago
Traffic: 1118 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6