of missing data
..calculating observed preservation values
Error in make.unique(rownames(datRef)) :
'names' must be a character vector
```
Here is a reproducible example with a fake dataset:
library(WGCNA)
setLabels = c("one", "two");
multiExpr
Order by: Relevance
there a maximum number of files that I can import using tximport? I'm receiving the error where the names must be the same length as the vector. I have looked at the other responses, and none have helped so far.
Thank you.
Laurie
updated 5.5 years ago • laurie.r.gray
exprs(esetSel), col = topo.colors(75), scale = "none", :
'ColSideColors' must be a character vector of length ncol(x)
Kindly help me regarding above error during construction of heatmap.
Thanks
 
updated 8.7 years ago • rkp
ENSBTAG00000004608
"617660" "407106" NA
"100138951"
# a named character vector with one NA
#now get symbols
syms <- unlist(mget(egs, org.Bt.egSYMBOL, ifnotfound=NA))
#throws and error...fair enough - need to drop the NA
which(egs == NA)
#gives named integer(0) - hmm
class(egs)
#gives [1] "character" - so I'm quite confused now.
NA %in% egs
#gives […
updated 14.2 years ago • Iain Gallagher
I have a strange error when I call ChIPQC.
> 'names' attribute [9] must be the same length as the vector [2]
Number in brackets vary depending on the number of samples.
RNFC81...Computing metrics for 9 samples...
list
Bam file has 194 contigs
Error in names(res) <- nms :
'names' attribute [9] must be the same length as the vector [2]
Calls: …
updated 4.6 years ago • ZheFrench
pre>
x <- findChromPeaks(raw, param = cwp)
Error in names(res) <- nms :
'names' attribute [12] must be the same length as the vector [6]</pre>
I don't understand the error above. I can't seem to...I think it may be an issue with the "processing" data in processingData, but how do I change it to a character since it's part of a S4 class object? Thanks!
<pre>
.…
7 x 7 in image
Using Sample as id variables
Saving 7 x 7 in image
Saving 7 x 7 in image
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 5.6 years ago • sonyuna90
data set used in the
vignette.
For the ALL list, I did the following. As ALL_Colorectal, all is a
character vector of Entrez IDs.
> entrezid = mget(ids, illuminaMousev2ENTREZID, ifnotfound = NA)
> all <- as.vector(as.numeric...did.
> pg=topTable(ebFit, coef=1, number=1000, p.value=0.05, lfc=1)
> de_pg <- pg[,5]> names(de_pg)<-pg[,3]
de…
Hi, I have a DNAStringSet list and I would like to convert it in a character vector but as.character does not work because it gives me a vector of "<S4 object of class \\"DNAStringSet\\">".
Could
updated 9.3 years ago • ribioinfo
I am trying to use the PAPi package but I get the same error all the time:
<pre>
'names' attribute [1] must be the same length as the vector [0]
In addition: Warning messages:
1: In if (getpath != 0) { :
the condition has length...Below is the head() of the data and below that is the papi() function. PLEASE HELP!!!!!!!
<pre>
Names Sample1 Sample2 Sample3…
updated 7.2 years ago • maryke.wijma
sample' (mc.cores = 32, mc.preschedule = FALSE)
[BSmooth] smoothing done in 17656.1 sec
Error in names(object) <- nm :
'names' attribute [25] must be the same length as the vector [2]</pre>
Here is the session info:
<pre>
> sessionInfo
nbsp; mode = "onDisk")
> mzs <- mz(raw\_data)
Error in names(res) <- nms :
'names' attribute \[50\] must be the same length as the vector \[25\]
In addition: Warning message:
stop worker...nbsp;
I understand the error occurs because the attribute/number of mzXML files is not same as the vecto…
lt;-read.delim("homologene.data.121212.data",header=FALSE) #
(date of file manually added to name when saving download)
colnames (homologene) <- c ("HomologyGroupID", "TaxonID", "EgID",
"Symbol", "ProteinGI", "ProteinAcc")
# Read rat...probesets that are on the array as Entrez IDs; this returns
a list which is converted to a character vector
# Next the probesets that don't have an Entrez…
kg.mouse = kegg.gsets("mouse")</pre>
I get the following error:
<pre>
Error in names(kg.sets) = paste(species, ks.names, sep = "") :
'names' attribute [1] must be the same length as the vector [0]
</pre>
or
<pre
t", row.names = FALSE)
files <- file.path(dir,"salmon_quant", samples$sample, "quant.sf")
names(files) <- samples$sample
tx2gene <- read_csv(file.path(dir, "tx2gene.gencode.v28.csv"))
txi <- tximport(files, type="salmon...getting is:
```
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13
Error in attr(x, "names") <- as.character(value) :…
updated 6.1 years ago • caranlove
2013 23:24
To: Hooiveld, Guido
Cc: bioconductor at r-project.org
Subject: Re: [BioC] annotationTools: character vector clean-up
You can try this:
library(stringr)
x <- str_replace(string=x, pattern=" /// .*$", replacement="")
stopifnot(!any(str_detect...lt;-read.delim("homologene.data.121212.data",header=FALSE)
#
> (date of file manually added to name when saving download) colname…
chipqc)
```
When I ran the function ChIPQC, I got the following error:
```
"Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", : 'names' attribute [9] must be the same length as the vector [7]"
```
I continued to run the ChIPQCreport
updated 6.2 years ago • analeigh.gui
__Edit__: One of my bam files has size 0 on disk!
I get the following error when I call summarizeOverlpas:
<code>Error in names(res) <- nms :<br/>
'names' attribute [15] must be the same length as the vector [2]<br/>
Calls: summarizeOverlaps ... .dispatchBamFiles -> bplapply -> bplapply -> bplapply -> bplapply<br/&…
updated 9.0 years ago • chriad
gene_len)
Error in nullp(tr, "sp", id = go_mapping, bias.data = gene_len) :
bias.data vector must have the same length as DEgenes vector!
How is it possible to fix it?
Thank you in advance
MakingNewOrganismPackages.htm
This are the dataframes and the commands I used:
> test3 GID Gene Name Protein Name
1 PSE\_0724 PSE\_0724 GCN5-related N-acetyltransferase
2 PSE\_0725 PSE\_0725 GCN5-related N-acetyltransferase...the argument 'x' in selecting a method for function 'unique': Error in structure(res, levels = lv, names = nm, class = "factor") : 'names' attribute \[16\] must b…
updated 11.0 years ago • artur
makeContrasts()
in the the limma package. The new argument will accept a set of
contrasts as a character vector,
thus facilitating the use of makeContrasts() within other functions
and the automatic construction
of
trouble when trying to make the annotation object.
According to the guides, you need to provide a named vector to the `` col `` argument in `` HeatmapAnnotation `` function, however I can't do that when generating dynamically...as there's different annotations. I've tried an un-named vector, but I get the following error every time:
<pre>
Error in ColorMapping(name = name, color…
updated 9.1 years ago • andrew.j.skelton73
listInputBam, genomeName="hg19")</code>
`` Get UCSC ensGene annotations. ``
<code>Error in names(trackIds) <- sub("^ ", "", nms[nms != "new"]) :<br/>
'names' attribute [210] must be the same length as the vector [209]<br/>
In addition: Warning...genome(session) <- "hg38"</code>
<code>> track_names <- trackNames(sessio…
updated 7.4 years ago • chrisamiller
After reading the csv file into R as a dataframe I have converted the first column with the IDs to a character vector, since the getBM() parameter, ___values___, requires a list of vectors as an argument. However, after running...getBM() function it outputs__ 0 observations of 4 variables, __thus not recognizing my character vector as the appropriate values to assigned the annot…
updated 7.2 years ago • agdif
div class="preformatted">I would like to know how to evaluate a character string as a variable
name
in R. Specifically, I need to "compute" the variable name in the
phenoData
slot of an ExpressionSet...class_label_factor <- sample.ExpressionSet$class_label
}
Here class_label is interpreted as a character string by R, but I need
for
it to be evaluated as a variable name. Seems straight…
updated 16.4 years ago • Kavitha Venkatesan
div class="preformatted">Hi,
is it possible to read a file for the sam calculation with the gene
names in the
same table.
The first column was with gene names, the next four were with
experiments and
the next 14 were the controls...this message:
Fehler in adjust.for.mt(data, cl, var.equal = var.equal) :
The length of cl must be equal to the number of columns of
data.
Zus?tzlich: Warni…
updated 19.9 years ago • Assa Yeroslaviz
ltr;">> rn<-rownames(tt)[tt$P.Value<=0.001]</p>
<p style="direction: ltr;"><strong>Those names are actually stored in a character vector, but I<br/>
need to convert it into a numeric vector:</strong></p>
<p style="direction
updated 9.8 years ago • libya.tahani
Hi good evening,
I want to replace special characters in row names (.30.) by (-30-)
for example:
`tag.30.gvs`
by
`tag-30-gvs `
for large data frame have more that 300 rownames all needs
updated 5.6 years ago • ph.shimaasherif
feature.type = NULL, sequenceRegionsAsSeqinfo = FALSE)
text: If con is missing, a character vector to use as the input.
But the argument does not seem to work, in fact I have looked into the source [https://github.com...file again or write it to a temporary file then import it. Is there any way to import gff from a character vector?
 
updated 8.2 years ago • Marlin
rbind(rd1, rd2)
RangedData with 6 rows and 0 value columns across 1 space
space ranges |
<character> <iranges> |
1 1 [1, 4] |
2 1 [2, 5] |
3 1 [3, 6] |
4 1 [1, 4] |
5 1 [2, 5] |
6 1 [3, 6] |
rd1 <- RangedData(IRanges(start=1:3,
end=4:6,
…
chr17', length(snps))
Error in validObject(.Object) :
invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed
character vector with no NAs
According to the man page this should be doable:
?`seqnames,GRanges-method`
seqnames...x), seqnames(x) <- value: Gets or sets the sequence
names.
value can be an Rle object, character vector, or factor.
# Try using an Rle…
alphabetToCodes[availableLetters], 0:(length(availableLetters) - :
'vals' must be a vector of the length of 'keys'
> traceback()
7: stop("'vals' must be a vector of the length of 'keys'")
6: buildLookupTable(alphabetToCodes
updated 9.5 years ago • Daniel Cameron
in validObject(.Object) :
invalid class “SummarizedExperiment” object: 1: invalid object for slot "NAMES" in class "SummarizedExperiment": got class "array", should be or extend class "characterORNULL"
invalid class “SummarizedExperiment...object: 2: 'names(x)' must be NULL or a character vector with no attributes
</pre>
I use this code:
<pre>
txi.kallisto <- tximport(s…
updated 8.0 years ago • jarod_v6@libero.it
div class="preformatted">Hi,
I try to get the vector of leaf's names from object "dendrogram"
generated by cut().
For example, I have a matrix mat(100*10)
rownames(mat) <- 301:400...dianaGenes))
dianaClusters.h3 <- cut(mydendrogram,h=3)
>From here, I tried to get the vector of leaf's names of subtree(
which are corresponding to rownames of mat) from
dianaClusters.h3$lower[…
updated 9.4 years ago • Ren Na
I am trying to apply `rma` from `oligo` package into data of file `GSE22247_non-normalized_data.txt` from this study: [GSE22247][1]
Did:
# read txt file into dataframe:
rawtxt <- read.delim(paste0(txtpath), sep='\t', skip = 4, header = T)
# convert dataframe into expression set:
rawData <- new("ExpressionFeatureSet", exprs = as.matrix(rawtxt))
# apply r…
On 08/07/2015 11:14 AM, tom carroll wrote:
You can provide your own annotation in the form of a named list of GRanges with the first element of the list containing a character vector of version.
I include an example below...You can also provide your own denovo List of GRanges but first
element must be a character with name "version".
library(GenomicRanges)
library(ChIPQC)
customAnnotati…
Error in setTrackXscaleParam(trackList[[1]], attr = "position", value = list(x = 122929700, : attr must be a slot name of xscale object
3.
stop("attr must be a slot name of xscale object")
2.
setTrackXscaleParam(trackList[[1]], attr
updated 5.7 years ago • liruiradiant
div class="preformatted">hi,
is it possible in R to use character strings to be written as x axis
ticks in a plot? for example i have a vector of values and i want to
plot them, is it possible...that for the x axis ticks not the index of
the value in the vector is used, but for example an "a" ("b" and so
on)
is written?
thanks, jo</div
updated 20.6 years ago • Dipl.-Ing. Johannes Rainer
div class="preformatted">Dear all,
Is it possible to use a string as an environment name in mget? I was
trying to do this with the following script, but it says that the
second
argument for mget is not an environment...Well, I know it isn't, since
it
was generated using paste function, so it's class is character.
> genes<-c("1007_s_at", "1053_at", "117_at", "121_at")
> c…
updated 18.8 years ago • Jarno Tuimala
gene of interest
This will be represented as a GRangesList, where each element in the
list is
a) named by the geneID
b) contains a GRanges of the coordinates, name and id of each
associated transcript
All of this information...for one or more geneIDs, you want
to ignore (for now)
that gene information, and just extract the names of all of the
transcripts. To do
this extraction, you must flat…
updated 12.2 years ago • Paul Shannon
fold change and ORA. I'm new to R generally, and continually run into an error that states my de names are not in the reference array (exact wording below) when I run the analysis.
I've done many checks, my data is clear...I can run the analysis on Graphite's online version of SPIA using the "all\_genes" and "sig\_genes" vectors/files listed below without any problem. I'd like to use R…
updated 10.9 years ago • A Eelmur
Hi there!
I'm writing some code to extract the [Accumulated Natural Vectors](https://doi.org/10.3389/fgene.2019.00234) from all the sequences in a DNAStringSet object. To speed things up I've...Hi there!
I'm writing some code to extract the [Accumulated Natural Vectors](https://doi.org/10.3389/fgene.2019.00234) from all the sequences in a DNAStringSet object. To speed things up I've writt…
updated 3.4 years ago • James
y = SNPMatrix, stats = "R.squared", symmetric = TRUE) :
STRING_ELT() can only be applied to a 'character vector', not a 'NULL'
#2
LD_matrix <- ld(SNPMatrix, depth = 100, stats = "R.squared")
Error in if (depth > dmax) { : argument is of length
FALSE)
> get(symb, org.Hs.egSYMBOL2EG)
Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
> class(symb[[1]])
[1] "character"
> length(symb[[1]])
[1] 4
> get(symb[[1]], org.Hs.egSYMBOL2EG...1] "6423"
Why is get() only giving me one entrez ID? Shouldn't it give me a
vector
of 4 entrez IDs when I pass it a vector of 4 gene…
doing GO graphing and I have done
> bpCutLeaves <- scan(file="343afterDupesNotCut.txt", what =
"character")
Read 343 items
> bpCutLeavestree <- GOGraph(bpCutLeaves, GOBPPARENTS)
> postscript ("bpCutLeavestreeTest.ps...I do
> nAttrs <- list()
> nAttrs$color <- scan(file="343forColorBB.txt", what="character")
Read 343 items
>…
div class="preformatted">Dear BioCers,
Anyone that could shed light on the error-
"Parameter names must by syntactically valid names in R"
-would be greatly appreciated.
Google turned up were these relevant findings...https://stat.ethz.ch/pipermail/bioconductor/2008-March/021440.html
-which suggested spaces in names could yield such errors. I failed to
find such spaces in my targets fil…
updated 15.6 years ago • k. brand
kavitha.venkatesan at="" gmail.com=""> writes:
> I would like to know how to evaluate a character string as a
variable name
> in R. Specifically, I need to "compute" the variable name in the
phenoData
> slot of an ExpressionSet...lt;- sample.ExpressionSet$class_label
> }
>
> Here class_label is interpreted as a character string by R, but I
need for
&…
Thanks Wolfgang and Arunava,
What I would like to do is the following:
I have the following character vector:
functionsUsed=c("myexpresso","mythreestep","myvsnrma","myl.farms","myj
ustPlier","mymmgmos","myexp.farms","myrma...etc
From a file, I read a 'listOfFunctions' character vector of unknown
length. This vector contains names like the ones given in
functionsUsed
vector: "myexpresso", "myvs…
and 7 value columns across 1 space
space ranges | type source phase strand
ID Name score
<factor> <iranges> | <factor> <factor> <factor> <factor>
<character> <character> <numeric>
1 2L [7529, 9484] | gene FlyBase 0 NA
FBgn0031208...textConnection(gff.str),asRangedData=FALSE)
Error in s…
updated 13.4 years ago • Malcolm Cook
data, when I upload csv files it always shows "Warning: Error in writeImpl: Text to be written must be a length-one character vector", anyone know what the warning means
updated 4.4 years ago • 15040356701
Could somebody advice me?
Here is the R:
library(SPIA)
x=topTable(fit,coef="WThypo",n=1003)
names(x)
names(x)
[1] "ID" "Gene.title" "Gene.symbol"
[4] "Gene.ID" "UniGene.title" "UniGene.symbol"
[7] "UniGene.ID" "Nucleotide.Title" "GI"
[10...x' in selecting a method for
function 'as.list': Error in .checkKeysAreWellFormed(keys…
updated 14.1 years ago • Jing Huang
x' in selecting a method for
function 'unlist': Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
Another approach fails too:
> selectedEntrezIds = select(org.Mm.eg.db...Error in .select(x, keys, columns, keytype = extraArgs[["kt"]],
jointype
= jointype) :
'keys' must be a character vector
I am not sure why I am getting this error as…
updated 11.1 years ago • Bade
hi i have two granges gr1 and gr2, i want a have score vector for each range of gr1 that is equal to width of its range. The values of score vectors are such that positions of gr1...overlapping with gr2 have must have score of gr2 on overlapping positions and zero on other positions
updated 9.8 years ago • vinod.acear
<div class="preformatted">Hi,
when analyzing more than 25 Affymetrix HGU133plus2 arrays the analysis
fails during background correction with GCRMA and the error message
says
"cannot allocate vector of 301.000kB ...."
I got the message ot only from my PC but also form a more potent
computer
(Ml570 G2, 4 CPU XEON MP 2.5/1Mb,
16 Gb...analysis
fails during background correction with GCRMA an…
updated 19.2 years ago • Ulrich Pfeffer
This is strange bug, even if the function isn't used correctly:
<pre>
library(Biostrings)
Warning messages:
1: package ‘BiocGenerics’ was built under R version 3.4.2
2: package ‘S4Vectors’ was built under R version 3.4.1
3: In eval(quote({ : bytecode version mismatch; using eval
4: package ‘IRanges’ was built under R version 3.4.1
5: undefined slot classes in definition of "XRaw":…
updated 7.5 years ago • ebiederstedt
similar classes. I would like to know if there is an efficient way to
collapse a CharacterList to a character vector of the same length,
such
that for elements of length > 1, those elements are collapsed with a
given separator...x[!is.na(x)] <- laply(x[!is.na(x)], str_c, collapse=sep,
.parallel=TRUE)
x <- as(x, "character")
}
x
}
-Ryan
</div
updated 11.7 years ago • Ryan C. Thompson
details:
call: match.arg(synchronous, c("off", "normal", "full"))
error: 'arg' must be NULL or a character vector
Error: package ‘org.At.tair.db’ could not be loaded
Kindly help me for above error
updated 9.4 years ago • rkp
1]] %in% lb, "orange", "grey")
label_color[is.na(label_color)] <- "grey"
names(label_color[label_color == "grey"]) <- "NA"
names(label_color[label_color == "organe"]) <- "lysosome
updated 2.4 years ago • Phương Thùy
fls <-list.files( bamDir, pattern="bam$", full=TRUE )
bamlst = BamFileList( fls, index=character(), yieldSize=100000,
obeyQname=TRUE )
SE<-summarizeOverlaps( exonicParts, bamlst, mode="Union",
singleEnd=FALSE, ignore.strand...nbsp; 'clear\_cluster' receive data failed:
reached elapsed time limit
Error in names(res) <- nms :
'na…
updated 6.9 years ago • A
div class="preformatted">Hi Carol,
carol white wrote:
> Hi,
> I
> want to multiply a vector (1st argument) by another vector or a
matrix
> (2nd argument) depends if a column or a row of a matrix or a subset
of
> a matrix...of the 2
> arguments) will be a vector of the length of the number of rows of
the
> 2nd argument.
Are you trying here to d…
Recent ...
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