param=params)
which reads in ok, but qa complains:
qa(lane1)
Error: UserArgumentMismatch
'lane' must be 'character(1)'
Is this because there is no function to handle BAM files? Or is this
some problem with the file itself or with
Order by: Relevance
my previous email, there is still one issue remaining
to be fixed in beadarray:setWeights function, namely:
>In the current implementation, if one passes a vector of weights (not
a list that contains one vector) to the function...all >the weights are
set to the **first element** of the vector, which is the direct result
of using wts[[1]] for the special case >of length(arra…
x) : is.na() applied to non-(list or vector) of type 'NULL'
4: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
5: In is.na(x) : is.na() applied to non-(list or vector...of type 'NULL'
6: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
7: In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'
8: In is.na(x) : is.na() applied to non-(list…
updated 10.1 years ago • Joseph Bundy
div class="preformatted">Hi,
Passing a list of weights, that has one vector of weights as the only
component,
to beadarray::setWeights causes R to aquire the entire available
memory.
After grabbing...array = 1);
BLData <- setWeights(BLData, wts = output$wts, array = 1);
Error: cannot allocate vector of size 389 Kb
In addition: Warning messages:
1: In class(x) <- NULL :
Reache…
updated 16.1 years ago • Mehrdad Shamsi
foreground = "MeanSignal",raw.data
=
TRUE, writeR = FALSE, targets)
Error: cannot allocate vector of size 13.7 Mb
In addition: There were 24 warnings (use warnings() to see them)
>
i got this error by using the package R.10.1
updated 15.8 years ago • neeraj rana
dataset is Ensembl_ID. You could use getBM function in
biomaRt
package to convert ensembl_ID to gene name or other IDs if needed.
Best regards,
Julie
On 1/19/11 2:10 PM, "Pablo Echeverria" <pablo.echeverria at="" unige.ch="">
wrote:
> Dear...that are described in your paper (those are
already
> working), but also I need to retrieve gene names associated to my
peaks.
&g…
updated 15.0 years ago • Julie Zhu
Hello,
Using the edgeR manual, I'm trying to follow the examples to run the goana function. I run the glmQLFTest (without any issues) and then use its output "qlf" as the input for goana or the topTags(qlf). I get the following errors.
```r
> qlf <- glmQLFTest(fit,coef=2)
> go <- goana(qlf, species="Mm")
Error in goana.default(de = DEGenes, universe = universe, ...)…
div class="preformatted">Dear all,
I can not change the list element names of my GAlignmentsList objects:
library(GenomicRanges)
library(Rsamtools)
ex1_file <- system.file("extdata", "ex1.bam...Rsamtools")
ga <- readGappedAlignments(ex1_file)
galist <- GAlignmentsList(one=gal, two=gal)
names(galist)
names(galist) <- c("three", "four")
Error in `names<-`(`*…
updated 12.2 years ago • Hans-Ulrich Klein
first time this happened to me:
```
> Peaks_TSS_all_hgnc<- getBM(filters= "ensembl_transcript_id", attributes=c("ensembl_transcript_id","ensembl_gene_id","hgnc_symbol"),values=Peaks_TSS_all$ClosestTSS_ID,mart= mart)
Batch submitting query [=============================>-] 95% eta: 2mError in getBM(filters = "ensembl_transcript_id", attributes = c("ensembl_transcript_id…
updated 4.1 years ago • alexandre.raposo
10.1101/2020.10.30.362533v1.full
Unfortunately, we recently didn't check for conflicting package names on CRAN and meanwhile a package with a similar name was accepted:
https://cran.r-project.org/src/contrib/Archive/rawr...ERROR
Maintainer: 'Christian Panse
<cp@fgcz.ethz.ch>'
New submission
Conflicting package names (submitted: rawR, existing: rawr [https://CRAN.R-project.org])
…
updated 5.1 years ago • Tobias
test.bw")
> import.bw(test_bw)
Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (9) or length
1
>
> traceback()
11: stop(wmsg(what, " must have the length of the object...test_bw, which = mini, as = "RleList")
Error in stop_if_wrong_length(what, ans_len) :
'ranges' must have the length of the object to construct (83…
updated 3.4 years ago • bonob
packages/release/data/annotation/
Almost Genome wide annotation packages following the name convention
org.species.eg.db. I'm wondering why org.At.tair.db is named
differently. Should its name be modified to
updated 13.5 years ago • Peng Yu
strand | exon_id exon_name exon_rank
<rle> <iranges> <rle> | <integer> <character> <integer>
[1] chr1 169795043-169795213 + | 26019 ENSE00001879003.1 1
[2] chr1 169798919-169798958 + | 26025 ENSE00003514372.1...ranges strand | exon_id exon_name exon_rank
<rle>…
updated 5.4 years ago • Dario Strbenac
affy to analyze some arrays, and I want to do mva plots.
I am trying to change the hybridizations names in the first row of the
exprSet, as I dont want to plot the PATH to my CEL files, but just a
legend.
I have tried to change these...names by accessing the elements of the
first row in the exprset, but I dont get them.
>exprs(L3hRMA)[0,]
/home/Genechip/LA_03h_02.CEL
and at the Genomic Analysis part, specifically on the CNV analysis I get this error __Error: vector memory exhausted (limit reached?)__, when trying to load the information about the abberant regions into a form of matrix
updated 7.4 years ago • rina
What
is reason for using ` vs ' or even "? Is there a resource that I can
use to look up special characters like this? I've searched through the
help files/etc. and no luck so far.
Thanks!
Matt
There were 42 warnings (use warnings
Hi,
I got `` Length of 'group' must equal number of columns in 'counts' `` with the below code.
> targets <- read.delim("phenoSp.txt", stringsAsFactors=FALSE...lt;- rbind(data, tot.counts=colSums(data))
>
> # inspect and look at the top row names!
> print("!!! data <- rbind(data, tot.counts=colSums(data))")
[1] "!!! data &…
updated 8.3 years ago • mictadlo
LFQ workflow of DEP package
data_results <- LFQ(comparison_table, expdesign, type = "all", name = "description", alpha = 0.05, lfc = 1)
When running the code, I get errors like :
Error: 'Protein.IDs' is not a column in 'comparison_table...impute.
-type
'all', 'control' or 'manual', The type of contrasts that will be generated.
-control
Character(1), The sample name to which t…
gt; rd1 = RangedData(ranges=IRanges(start=runif(4, min=1, max=10E8),
width=runif(4, min=1, max=10E5), names=paste("bla",1:4)), space=1:2)
> rownames(rd1)
[1] "bla 1" "bla 3" "bla 2" "bla 4"
> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0...RangedData with 4 rows and 0 value columns across 2 spaces
space ranges |
<character…
updated 15.8 years ago • Michael Dondrup
of every protocadherin gene. The `` select `` function has a `` keys `` parameter which requires a character vector. Instead of manually finding which elements have the PCDH suffix
<pre>
> symbols <- keys(org.Hs.eg.db, "SYMBOL
updated 9.5 years ago • Dario Strbenac
gt;> Error in .setSeqNames(x, value) :
>>>>> The replacement value for isActiveSeq must be a logical vector,
with
>>>>> names that match the seqlevels of the object
>>>>
>>>> The error message...ATC
L
>>> varAA txID geneID …
genes. However, after the loading the sequences and gff file, the check input command returned " Names of list elements in 'seq' and 'annotation' must match". i have specified the path to both gff and fasta files using
gff_dir...using
check_input(aastringsetlist, grangeslist)
Error in check_list_names(seq, annotation) :
Names of list elements in 'seq' and 'annotation' must match.
…
updated 24 months ago • Sujeevan
but I would appreciate if someone
could
point me at the right function(s) to use:
I have two vectors containing all GO terms associated with proteins
retrieved in two proteomic experiments and would like to figure
updated 18.8 years ago • Johannes Graumann
library(org.Hs.eg.db)
library(DOSE)
library(ReactomePA)
## feature 1: numeric vector
geneList <- d[,2]
## feature 2: named vector
names(geneList) <- as.character(d[,1])
print(geneList)
## feature 3: decreasing order...geneLIST <- sort(geneList, decreasing = TRUE)
head(geneList)
But when I try to name the vector I obt…
updated 5.6 years ago • camillab.
error.
#This is the warning I get.
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to use
only letters, numbers, and delimiters..._' or '.', as these are safe characters
for column names in R. [This is a message, not an warning or error]
More Importantly, the following …
updated 7.0 years ago • evocanres
lt;- list(NULL,NULL)
## Error in base::colMeans(x, na.rm = na.rm, dims = dims, ...) :
## 'x' must be an array of at least two dimensions
```
I'm using BiocSingular 1.16.0 and I don't see anything weird in the data, the process...or the traceback:
```r
traceback()
16: stop("'x' must be an array of at least two dimensions")
15: base::colMeans(x, na.rm = na.rm, dims = dims, ...)
14: …
updated 2.5 years ago • Lluís Revilla Sancho
After the recent update to R 3.4.0, updates and installation of several Bioconductor packages return a warning during installation -- specifically, there seems to be an issue in how BiocParallel sets up its core classes:
<pre>
Warning in is.na(x[[i]]) :
is.na() applied to non-(list or vector) of type 'environment'
'BiocParallel' did not register default BiocParallelParams:
invalid …
updated 8.5 years ago • nhejazi
Hello ...
I have the following chromosome names in my hg19 reference sequence.
<pre>
> names(seqlengths(tx_by_gene))
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8"
[9] "chr9" "chr10...Hello ...
I have the foll…
updated 11.2 years ago • marcovth
filtering bam file: RE: MEDIPS.createSet
error
And yes, the argument BSgenome is supposed to be a character string
naming the BSgenome object. Please let me know, if this will work for
you.
Lukas
P.S. I like the chr.select=seqnames...I do this, the literal BSgenome.Ptrichocarpa.Phytozome.v3 is
assigned to the BSgenome variable as a character vector. So instead, I
do this:
BSgenome = BSgenome.Ptr…
div class="preformatted">Hi everyone,
Does anyone know how to go from gene name to ENSEMBL ID?
I'm using lumi to analyze my microarray data, however the names get
changed from NuID to gene name when reading
updated 12.2 years ago • Kripa R
<div class="preformatted">Dear All
I have GRanges objects of transcript information (subject) & for
regions of
interest (query).
Top lines of (subject):
seqnames ranges strand | tx_id
tx_name
<rle> <iranges> <rle> | <integer>
<character>
[1] 1 [5473, 16844] + | 1
ENSRNOT00000…
updated 12.7 years ago • Tom Oates
some on
virulence plasmids). The GAL file does not contain any genbank IDs.
It does contain locus names. The gpr files I have do not contain the
locus name, but instead has a name that is just used in the chip I
believe. The genbank...files for KIM and CO92 contain the locus names,
and of course the genbank IDs. (ie In the GPR file the name of a gene
is, for example, NTORF3478. In the gal fil…
updated 20.7 years ago • Palmer, Lance
se, design = design, ignoreRank) : counts matrix should be numeric, currently it has mode: character
se, design = design, ignoreRank) :
counts matrix should be numeric, currently it has mode: character
Thanks,
Molly
```
Samples<-c("MM-0017-RNA-T-07", "MM-0623-RNA-T-01", "MM-0039-RNA-T-06")
inputs<-list()
for (i in 1:length(Samples)){
inputs...i]] <- paste0("/data1/users/molly/", "ciri_out/", Samples[i], ".ciri.output")
}
names(inputs) <- Samples
…
updated 3.1 years ago • molly.fraser
<div class="preformatted">I just came back from a vacation. Another user has complained about
this. I will
take a look when I get to the office on Monday.
Thanks
>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>X-IronPort-Anti-Spam-Filtered: true
>X-IronPort-Anti-Spam-Result:
AmABAMfC8kmBhJEPlGdsb2JhbACNNIkhAQEBAQkLCAkRBad…
plantula <- readFastq("s6_plantula.fq",
qualityType="SFastqQuality")*
*** Error: cannot allocate vector of size 649.8 Mb*
*
*
* *
* Then i **set memory.size() at 3000 as well as memory.limit() but i'm
already having the problem*
* i has a processor
updated 15.4 years ago • Marco Ortiz
ENSG00000000003 ENSG00000000005 ...<br/>
ENSG00000281912 ENSG00000281920<br/>
rowData names(3): ensembl_gene_id external_gene_name<br/>
original_ensembl_gene_id<br/>
colnames(521): TCGA-3L-AA1B-01A-11R-A37K...11R-A155-07 ...<br/>
TCGA-AA-3675-01A-02R-0905-07 TCGA-G4-6323-01A-11R-1723-07<br/>
colData names(101): sample pati…
updated 8.1 years ago • svlachavas
div class="preformatted">Hi,
I am having problems in finding the marker names in a flowFrame.
(The marker names mapped onto the channel names - i.e.FL1-H, FL2-H,
FL3-H
and FL4-H).
I wrote the code:
FCS <- read.FCS...subfilesdir2)
FCS
featureNames(FCS)
and got this output - but it does not seem to show any new names (i.e
CD45),
so am I doing the right thing:
flowFrame object 'P:/Pro…
updated 17.6 years ago • Anne
am not sure whether it means "cryptocephal" or "Calreticulin".
I found a description that the gene name of drosophila starts with lowercase if named for recessive mutant and uppercase if named for dominant mutant. But it...to tell when I searched the homepage...
Is there any good way to detect the correct official full name? Or is there any way to get an annotated file with both gene symbol a…
updated 3.7 years ago • Chise
Error in parse_pd_for_read_fs(files, path, pattern, phenoData, sep, as.is, :
Argument 'phenoData' must be of type 'AnnotatedDataFrame' or a filename
of a text file containing the phenotypic information
```
As I do not know much
updated 5.1 years ago • Rainer
How to get gene names for the probe id's using
<pre>
pd.hta.2.0?</pre
updated 7.2 years ago • sunandinisharma
CEL files. I have the expression values and
the colnames extracted as matrix files. The colnames
are named with the .cel file names. Now in a different
file the .CEL files are referenced to sample name. I
am interested in classifying...I can
define certain files (as patterns) as one go and
classiffy them as some category. The file names are
unique with numbers and doe not seem to have specific
p…
The matrix looks like this:
> mat
$genotypes
A SnpMatrix with 10 rows and 50581 columns
Row names: Rodriguez_Lizard_1240_sequence_1_pileup.txt ...
Rodriguez_Lizard_623_sequence_1_pileup.txt
Col names: RADid_0000001_depth_39...50581 rows and 4 columns
snp.names allele.1
allele.2 ignore
<character> <dnastrings…
labels on multiple lines, one line pr. item, which is better if working with large lists/long character vectors.
Please see example below.
library(ggvenn)
d<-data.frame(id=paste(LETTERS[1:9]),
A=c(TRUE,TRUE,TRUE,FALSE,FALSE
header=TRUE)
# we want the log2 fold change
original_gene_list <- df$log2FoldChange
# name the vector
names(original_gene_list) <- df$X
# omit any NA values
gene_list<-na.omit(original_gene_list)
# sort the list...significant results, we want to filter on log2fold change
genes <- sig_genes_df$log2FoldChange
# Name the vector
names(genes) <- sig_genes_df$X…
updated 3.8 years ago • beslinail
for the prostate cancer, and have managed to extract the counts using assay(). The column names of the dataframe extracted however, whilst they look like identifiers, bear no resemblance to any identifiers in the...TCGA database.
I have a separate download of clinical data, with TCGA identifiers and sample names for the same data set. How does one link up columns in the assay with known sample n…
updated 8.4 years ago • b.curran
called "myeset"
According to the guide I need to pass to sam
the data (myeset in this case) and a vector cl
This is a one class case, so
so cl must be a vector of ones of length equal to number
of sample.
As the number of sample is
updated 21.0 years ago • Edoardo Saccenti
Hi all,
It looks as if the as.vector call to a run length encoded factor turns
it to a vector of characters.
Did this happen on accident, or was it a deliberate design decision?
Previously:
R-2.12, IRanges_1.7.19...Now:
R-2.12, IRanges_1.7.31, GenomicRanges_1.1.20 (The factor is converted
to a character)
R> a <- Rle(strand(c('+', '-', '+', '+', '-')))
R> as.vector(a[1])
…
<div class="preformatted">Dear All,
Appreciate your time. Need your expertise. I am trying to use GOSeq
for GO analysis of my RNA-seq experiments.
I was using Tophat->Cufflinks for DE, and mouse mm10 for annotation.
I am trying to build the gene length database by myself, given that
the current version of goseq does not support the mm10 build.
1, Cufflinks seems ignored the origi…
updated 12.6 years ago • Xulong Wang
gt; affyQAReport(Rawdata)
(loaded the KernSmooth namespace)
Error: cannot allocate vector of size 206.7 Mb
In addition: Warning messages:
1: In KernSmooth::bkde2D(x, gridsize = nbin, bandwidth = bandwidth) :
Binning
updated 5.8 years ago • manuchandwadkar
<div class="preformatted">Hi,
I am using the GenomicFeatures package to extract exons from a
transcript
database file. I am using the ensembl transcript database which has no
chr,
yet my bam files that I am working have the chr prefix.
I was thinking one could append chr to the seqlevels in the transcript
database like this:
library('GenomicFeatures')
txdb <- loadDb(txdbFile)
newS…
updated 11.5 years ago • Fong Chun Chan
classes, fdef, mtable) :
unable to find an inherited method for function ‘path’ for signature ‘"character"’
!> sessionInfo()
R Under development (unstable) (2014-12-03 r67101)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale
updated 11.1 years ago • Kipper Fletez-Brant
Hello,
I performed an analysis of differential expression with SAM method, obtaining the genes that are up and down. I used these scripts:
<pre>
> samfit = SAM(exprdc, group, resp.type="Two class unpaired", fdr.output=.01)</pre>
<pre>
> sigSAM_low = as.numeric(samfit$siggenes.table$genes.lo[ ,2])</pre>
<pre>
> sigSAM_up = as.nume…
updated 10.4 years ago • santi.cabellos
<div class="preformatted">
I'm trying to use edgeR to analyse RNA-seq data following the guidance
of "edgeR: differential expression analysis of digital gene expression
data".
I have done exactly as the manual told and when tapping the command "d
<-
DGEList(counts=d, group=group)", then an error comes as
"?????????DGEList(counts = d, group = group) :
Length of 'group' must equal nu…
c('nutrients','yes','no'))</pre>
And the same for the 'snail' treatment, with the argument
<pre>
name='nutrientsyes.snailyes'</pre>
for the interaction. This returned reasonable results. However, I was exploring the...no')</pre>
2.
<pre>
contrast=c(0,1,0,0)</pre>
3.
<pre>
name='nutrients_yes_vs_no…
updated 10.3 years ago • ryan.mcminds
div class="preformatted">Chuck,
This was an oversight on my part. I was focused on long Rle vectors
and
didn't fully test when the 'times' argument was an integer vector with
the same length as 'x'. I just checked in a patch
with the baseMean, log2 fold change, and pvalues, except that the rows are numbered rather than named by gene.
I would assume that the genes are listed in the same order that they appeared in the countData, ie I could annotate...the results file with gene names by simply assigning it the countData row names. I hesitate to do this, however, in case some other ordering occurred
updated 8.5 years ago • kalaga
snps = getSNPlocs(c("ch1","ch2"),as.GRanges=T)
renamed.levels = gsub("ch","chr",seqlevels(snps))
names(renamed.levels) = seqlevels(snps)
snps = renameSeqlevels(snps,renamed.levels)
#CDS grouped by gene
gene.list = cdsBy(txdb19...call gives this error:
Error in .setSeqNames(x, value) :
The replacement value for isActiveSeq must be a logical vector,
with
names that match the seqlevels of the…
updated 13.9 years ago • Alex Gutteridge
updateObject(toll10b_k27ac_2to4h_1.ranges, verbose=TRUE)
updateObject(object = 'GRanges')
Error in names(ans) <- seqnames(x) :
'names' attribute [12] must be the same length as the vector [0]</pre>
I can provide a download link for the saved
updated 11.1 years ago • Jeff Johnston
SYMBOL...
> Error: 2 errors; first error:
> Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x), : 'data' must be of a > vector type, was 'NULL'
I am wondering if this issue is related to an error to the GEOquery
updated 11.7 years ago • Guest User
Hello, I have a problem using the function getBM in BioMart. I am using this command:
library(biomaRt)
ensembl = useMart("ensembl",dataset="drerio_gene_ensembl")
Result<- getBM(attributes=c("ensembl_gene_id","external_gene_name"), filters = "go", values = 'GO:0005856', mart =ensembl)
But sometimes R return me this error:
Error in getBM(attributes = c("ensembl_gene_id", "externa…
updated 6.5 years ago • lbuo
Recent ...
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