columns across 1 space
space ranges | IN1 stable_id
strand
<character> <iranges> | <character> <character>
<integer>
1 13 [92020005, 92901611] | 4448480 ENSMUSG00000021708
-1
biotype status
<character...character>
1 protein_coding KNOWN
description
<character>
1 RAS protein-s…
Order by: Relevance
Can
anyone help?
- Paul
Error in as.numeric(hgsid) :
cannot coerce type 'externalptr' to vector of type 'double'
> traceback ()
5: browserView(<s4 "ucscsession"="" class="" object="" of="">, <s4 "genomesegment"="" class="" object="" of="">)
4: browserView
updated 16.9 years ago • Paul Shannon
error:
> plotMA3by2(RG2, device="pdf")
Error in MA$weights : $ operator is invalid for atomic vectors
Calls: plotMA3by2
Execution halted
I have managed to successfully generate a box plot and a HCA on the
normalized
updated 14.5 years ago • Richard Green
lt;- filterFFT(cover_data, pcKeepComp=0.02, showPowerSpec=TRUE)
Error: cannot allocate vector of size 878.2 Mb
```
</rle></iranges></rle></rle></iranges></rle
updated 6.0 years ago • anne.kannengiesser
TRUE, start=1, end=23)
Error in .normarg\_field(start.field, "start") :
'start.field' must be a character vector with no NAs
> gr1 <- makeGRangesFromDataFrame(MPB, keep.extra.columns=TRUE,
+  
updated 10.6 years ago • achimmiri
are working wonderfully to get some signatures, but for others objects I do not manage to build the vector and the results are two different kind of Errors (depending on the VRanges objects I try to concatenate).
Here is...combine_CompressedList_objects(class(x), objects, use.names = FALSE, :
the objects to combine must be CompressedList objects (or NULLs)</pre>
…
updated 8.3 years ago • guillaume.dachy
advice about where i am going wrong with a loop i'm trying to write for cleaning up UNIPROT data names.
Basically, the name i have from proteomics analysis is something like tr|A0A02DLI66|A0A02DLI66\_MYTGA but i would
updated 7.2 years ago • laural710
PM
To: r-help
Cc: bioconductor
Subject: [BioC] colnames and get means for the columns with the "same"
names
hi,
I have a conversion table for colnames like this:
Probe_ID HUMAN_LLID
1 AF106325_PROBE1 7052
2 NM_019386_PROBE1...colnames to another ID's system, HUMAN_LLID by
using the table. The colnames of x1 with the same names (in
HUMAN_LLID) need to be averaged. Is there a good…
<div class="preformatted">Hello friends,
i am working on some SMD two color data for Toxoplasma gondii , i have
done differential expression analysis. Now i want to annotate these
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 want to an…
updated 15.0 years ago • Budhayash Gautam
Hello,
I am using DESeq2 to perform LRT analysis. I have 4 conditions, and each group named Group1, Group2, Group3, and Group4. Each group has 80 to 100 samples. I use only p-adj value to determine DEGs.
Whenever I use...function, the last group (like group4) has distinctive characteristics.
When I changed the group name (group3 to group4, group4 to group3), DEGs were changed. (common DE…
updated 6.2 years ago • minyoungcho93
entries to the LOCUS IDS mapping on it.
LOC: This are the AffyIDS and the corresponding LOCUS IDS, a vector.
It
comes from applying hgu133aLOCUSID to a set of AffyIDS.
The function looks for the Locus IDS (LOC) in the entries of...lt;-function(GOLOCmap,LOC)
{
LOCs<-sort(LOC)
maximum<-max(LOCs)
output<-as.list(1:length(names(GOLOCmap)))
res<-0
for (i in 1:length(names(…
the SAM_ANNOTATION function of lapply(), I am unsure if allGenes.hs is right. The allGene.hs is my named vector containing all of my genes and the p-values.
Please help
updated 2.7 years ago • Priya
I created two comma delimited texte files from the excel
spreadsheet: 1. phenoData with group names and covariate information
and 2.
expression data. I used the read.table function to create two
data.frames
in R: xxCov...and xxData. I tried to use the new() function to create a
"phenoData" object from the xxCov and a vector covN with varLabels. I
get
an error message "Invalid 'phenoData' objec…
<div class="preformatted">Dear list,
I am using the Rgraphviz new interface (layoutGraph + renderGraph) to
plot graphs. I want Custom node sizes with nodeRenderInfo, it simply
does not work. Has anybody get through this problem? Any
suggestions/ideas will be appreciated.
#Note: labels, shapes, widths & heights are all vectors of the length.
For shapes, I used either box, reactangle…
files)]
if (length(CDFfile) != 1)
stop(paste("CDFfile is not specified,exactly one CDF file must
exist in path.\n"))
if (is.null(CELfiles))
CELfiles <- files[grep(".[cC][eE][lL]", files)]
nchips <- length(CELfiles)
if (nchips < 1)
stop...else {
if (length(chip.names) != nchips) {
warning("Not the same number of chips than chip names. Assigning
n…
I just installed monocle package to analyze some data. When I ran the example in package which names "HSMM\_analysis.R" to learn to use monocle, Rscript reported a bug:
<pre>
Error in argfun(start + i - 1L) :
no slot of name "expressionFamily
In trying to create a contrast matrix of interest, I thought it would
be easier to assign one-word names to the different disease states. I
seem to have gotten it to work for the GDS3715 data set that happens
to be a 3x2 factorial
TRUE, plotDendrograms=FALSE)
I tried colorLabels=FALSE and nothing changed.
I tried ySymbols=names(MEs) which gave an error that the number of ySymbols must match the number of rows in the adjacency matrix.
I tried to figure
I'm working with a non-model species so having genes' name is luxury I can't afford. I have my design matrix and choose one combination I'm interested:
cont.matrix1 <- makeContrasts...summa.fit)
and when I wanna see the volcano plot:
volcanoplot(fit.cont,coef=1,highlight=100,names=fit.cont$ !!!!!! , main="B.PregVsLac")
in fit.cont$, there is no list of the transcript IDs there so I …
updated 3.0 years ago • Mohammad
Dear Community,
I am reading a single cell file and processing it along with TSNE. Finally generation of loom files.
The commands that I am using to read file is :
<pre>
loadSCE <- function(path){
sce <- scater::read10XResults(path)
#sce <- normalize(sce) # Data normalization based on scran
mitochondrialG…
updated 7.0 years ago • Abhishek Singh
rawdata, filenames = identFile, verbose = FALSE)
Error in basename(id$spectrumFile) : a character vector argument expected</pre>
Any suggestions on how to get past this will be appreciated! I am new to proteomics
updated 11.0 years ago • queso012
and I am trying to get new version of GO
and I could
not find it.
> GOLocmap<-mget(names(myGOCC$intCounts),GOALLLOCUSID);
Error in mget(names(myGOCC$intCounts), GOALLLOCUSID) :
Object "GOALLLOCUSID" not found...of:
Source
This will be fine for almost all users
Error in match(pkgs, libPkgs) : match requires vector arguments
Please ,let me know if anyone did this before?
…
I have a GRanges object called "MmOrganismDbTxs" that has a CharacterList of UCSC-style names as one of the metadata columns, and I have a vector of UCSC-style names that I'm interested in called "desiredUCnames". I would
updated 10.1 years ago • efoss
case there is even one
package that is expressly for microarray / gene expression data: the
package name is plsgenomics - you can download it from CRAN and it
will take your data as is (experiments in columns, genes in rows).
Also...info you have for each experiment become the predictors (Xs). I
would combine the cell percentages vector and any other Xs you want to
look at into a data.frame (yo…
updated 17.3 years ago • Amy Mikhail
with the reactome.db package: in version 1.50.0 most of the pathway IDs are not mapped to pathway names:
library( reactome.db )
reactome.list <- as.list( reactomePATHID2EXTID )
have.name <- names( reactome.list ) %in% ls( reactomePATHID2NAME...In 3.1.2 with reactome.db 1.50.0 only 1518 of 10373 pathway IDs can be mapped to a pathway name, while in R 3.0.2 with reactome.db ver…
updated 10.7 years ago • Johannes Rainer
preformatted">Dear list,
I have gene expression data with probeset IDs & gene set data with
gene names. So both gene set and expression data are not using the
same gene ID system. Both gene set and expression data should use...is a requirement of the GAGE analysis.
So the problem is that if i convert the Probeset IDs to gene name, i
get a single gene name for multiple probes. So the ex…
When using DESeq2 in the past, count data and normalized count data, etc... retained the names of samples indicated in the first column of the colData table.
I've used dds = DESeqDataSetFromMatrix(countData..._001 Day1AirDEMED DEMED Air 1
I expected the names of the columns in my count matrix from DE…
updated 9.5 years ago • jshouse
val, :
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
Called from: getBM
updated 5.9 years ago • frank007
I wonder if anyone has come across the same problem as I am having.
I am trying to map a gene name i.e HGNC symbol to its corresponding
affymetrix probe using R/Bioconductor but I don't seem to be able to
do it using biomaRt
does not seem to have a valid repository, skipping
Error in agrep(nfPkgs[i], availPkgs) : pattern must be
a non-empty character string
In addition: Warning message:
Failed to read replisting at
http://www.bioconductor.org
1) get the sequence
2) do the calculations
3) plot the results and
4) use the sequence name (names(rs) in plot legends and titles,
e.g.
plot(x, main = paste(sequence_name, 'in condition X'), sep = '
').
The name I want to use is the first...function(x){
name = strsplit(names(x), split = ' ')[[1]][1]
seq = strsplit(toString(x), split = ',')[[1]][1]
names(seq) = name
re…
updated 13.5 years ago • Kemal Akat
Greetings,
I'm working on RNA-Seq analysis from dog (Canis Familiaris) samples and I'm using the last genome annotation data available (CanFam3.1) from NCBI (https://www.ncbi.nlm.nih.gov/genome?LinkName=assembly\_genome&from\_uid=317138).
When I use the following code:
<pre>
txdb <- makeTxDbFromGFF(gtffile, format = "gff3", circ_seqs = DEFAULT_CIRC_SE…
updated 8.7 years ago • jggomeza
DataFrame with 6 rows and 3 columns
ID Symbol Type
<character> <character> <character>
ENSMUSG00000061195 ENSG00000186092 OR4F5 Gene Expression
ENSMUSG00000093804 ENSG00000284733...DataFrame with 6 rows and 3 columns
ID Symbol Type
…
updated 23 months ago • Dario Strbenac
Hi
Can anyone please guide me on plotting a graph showing the gene names of top differentially expressed genes in edgeR ?
 
updated 8.2 years ago • fawazfebin
library(GenomicRanges)
\#\#\# constructing a GRanges object and adding names afterwards works well:
myGR <- GRanges(seqnames=c("chr1","chr2"), ranges=IRanges(start=c(100,200), width=100))
names(myGR) <- c("region1...region2")
myGR
\#\#\# but I can't add names when I construct the object. That gives me a column in values(myGR\_2) called "names". Not quite what I …
updated 10.3 years ago • Janet Young
ranges strand | ENSG pval dPSI
<rle> <iranges> <rle> | <character> <numeric> <numeric>
1 chr1 167012370-167012510 + | ENSG00000143194 0.0000000 1.000000
2 chr1 186304109-186304256...lt;- getSeq(BSgenome.Hsapiens.UCSC.hg38, gr_up)
DNAStringSet object of length 376:
width seq …
updated 3.8 years ago • Liliian
gene expression array, but if you could just point
me into the direction where to find those names for whichever chip and
any associated libraries or files I need.
Many thanks for any clues.
Julia
-- output of sessionInfo
updated 13.1 years ago • Guest User
Time_Cond3D_Ipsi.SexM" "Time_Cond4W_Ipsi.SexM"
res <- results(dds, name="Time_Cond4W_Ipsi.SexM", cooksCutoff=TRUE, filterFun=ihw)
results_apeglm <- lfcShrink(dds, coef="Time_Cond4W_Ipsi.SexM...pvalue padj symbol
<numeric> <numeric> <numeric> <numeric> <numeric> <character>
ENSMUSG00000005237 19.8251 …
if (length(num) < 1 | sum(is.na(num)) > 0)
stop("Please check your parameter names, which must match the
\n
\n colnames of phenotype files.")
targetsFile <- targetsFile[, num, drop = F]
nchip <- ncol(expr)
targetSort...targetsFile[,
num, drop = F]), , drop = F]
The parameters argument specifies the column names in t…
updated 16.3 years ago • Dick Beyer
2021-03-30 22:06:50
Error in validObject(.Object) :
invalid class "SummarizedExperiment" object:
'names(x)' must be NULL or have the length of 'x'
```
The rnaseq_samples.csv is a csv file with three columns labeled "names", "files", and...checked to make sure the filepaths weren't the problem. I also double-checked that the samples under "names" were characters and not numeric since a co…
updated 4.7 years ago • dshres
I'm using the gometh() function of missMethyl and am trying to pull out the names of the differentially methylated genes from the output table, which looks like this:
```
go <- missMethyl::gometh(sig.cpg...is the number of genes that are differentially methylated. How do I find out, for example, the names of the 5 differentially methylated genes for GO:0015748?
Thanks, Stewart
updated 5.3 years ago • stewart999
e = makeXMLError(msg, code, domain, line, col, level, filename,
class)
dom = names(e$domain)
class(e) = c(names(e$code), sprintf("%s_Error", gsub("_FROM_",
"_", dom)), class(e))
if (e$code == xmlParserErrors["XML_IO_LOAD_ERROR...stop(e)
})("failed to load HTTP resource\n", 1549L, 8L, 0L, 0L, 1L, character(0))
16: .Call("RS_XML_ParseTree…
updated 7.9 years ago • enricoferrero
Hi,
is there any way to extract the whole clustering structure of the all the nodes in the containers created with the command 'nesthc'? I would like to have something like two mapping vectors specifying for each node in the graph the 1st- and 2nd-level on containers in which they are clustered.
So if I have a graph...containers created with the command 'nesthc'? I would like …
retVal <- retVal[retVal[[geneID]] %in% feasibleGenes, ]
## split the table into a named list of GOs
return(split(retVal[[geneID]], retVal[["go_id"]]))
}
```
I created a custom OrgDb (for a non-model organism) using `AnnotationForge...and found out that custom OrgDb files created using `AnnotationForge` seem to have uppercase field names like SYMBOL and ENSEMBL in the…
updated 6.8 years ago • psutton
used is arabidopsis tiling array 1.0R. However,
I have
problems to extract probe sequence and probe names from bpmap files
provided
by affymetrix. I also tried to write a tpmap file. But it doesn't
seems to
contain the probe names
div class="preformatted">Dear all,
How to filter genes from the expreSet by using the probe set names
(affy)? Anyone has any clue on it? Thank you!
Xin LIU</div
also without luck. bpiterate is "unable to input data, can't coerce S4 class into vector". bpvec produces an error because the output vector length doesn't match the length of the vector for the starting...X) :
no method for coercing this S4 class to a vector
Calls: local ... doTryCatch -> bpok -> vapply -> as.list -> as.l…
updated 8.0 years ago • s.munster
1 page):** Must contain information for at least 3 references. For each reference, the following information is to be provided: Name, title...etc.). Should include the PhD advisor as one reference. If that’s not possible, a short explanation must be provided for stating the reason (retirement, inaccessibility, etc.) for the exclusion, in this document.
**3) CV (4 pages maximum...Must contain a…
updated 2.7 years ago • yuzun
contains entries like this one: "exm-rs1003581-131_B_F_1990477648") another column which contain names (some are in this format "exm-rs1003582" and some are in this "exm-IND6-167673849"). Other columns contain chromosome, AddressID_A...GWAStools to analyze this data. GWAStools requires for the AnnotationDataset a snpID variable which must be an integer, but that does no correspond with the SNP ID…
updated 4.1 years ago • Adrián
__Error in .check\_arg\_names(width, "width", x\_names, x\_names.label) :
when 'width' has names, they must be identical to 'seqlevels(x)'__
I recently updated my OS and installed R and Bioconductor more recent versions
has the same start and end coordinates, but the CHR column shows chromosomes 1 and 2. One of these must be incorrect.
I noticed the chromosome name format changed from 'chrX' to just 'X', and I imagine that has something to do with
updated 7.2 years ago • jingyaq
samp.idx]-rowMeans(cnts.norm[, ref.idx])
</pre>
where 'ref.idx' and 'samp.idx' are the numeric vectors of column numbers for the reference and target conditions respectively.
In the example taken in this workflow, the...sample (column 2). So I get the 'ref.idx' and 'amp.idx' based on pattern matching in the column names as follows:
<pre>
> cn=colnames(cnts)
> ref.i…
objects being input, what is the best way to coerce to a `data.frame`? I would like to keep column names in the current gene symbol format. They might have unusual symbols like HLA-A, for example. `as.data.frame` automatically...converts column names to by syntactically valid, by doing things such as replancing hyphens by periods. `data.frame(myDataFrame, check.names
updated 4.6 years ago • Dario Strbenac
ExpressionSet object is
intended to be created parsing a matrix expression data with duplicate
row names:
> try(myExpressionSet <- new("ExpressionSet", exprs = myexprsunique,
phenoData = myphenoData, annotation = myannotation...I was wondering if there exists a way to create this ExpressionSet
object although duplicate row names exist in the expression matrix
data parsed? Many than…
updated 14.2 years ago • nqueralt@clinic.ub.es
Enter the body of text here
Dear, everyone.
Currently, I am doing find out DMPs in Champ using Illumina EPIC methylation array. And I am doing case-control studies
But I got the error message Error in champ.DMP() : ChAMP.DMP Have not detected even one significant CpGs. You may try other threshold. Then I found the reason why I got the error message due to the Benjamini-Hochberg correction, and…
updated 2.1 years ago • 486342583
an error while using "samples" argument in
> "readCtData". I am basically trying to use sample names from a
design file
> column rather than using file names.
>
> raw <- readCtData(files=files$FileName, path=path, SDS=TRUE...as.is=TRUE), then the content of each column is
probably a
factor rather than e.g. numeric or character. Does it work is you
say?:
raw &a…
updated 14.9 years ago • Heidi Dvinge
batch)
(FYI, "exprdata" exists in memory as a 22283x919 double matrix, and
"batch" is 919 x 1 character matrix with the GEO dataset name, e.g.,
"GSE1456")
However, an exception is being thrown in ComBat which reads as
follows...Ranked by U.S.News & World Report as one of America's "Best Hospitals"
in 13 specialties. Named to FORTUNE? Magazine's "100 Best Companies to
Work For?" list ei…
phenotype data, i received an error message when trying rma(my data). the message says differing names of the CEL files between phenoData and protocolData. However I don't see any obvious difference in names. I pasted my flow
updated 11.2 years ago • bin.shan
NULL))
but I received this error message:
Error in "[<-"(`*tmp*`, , i, value = structure(list(), .Names =
character(0), row.names = c("1", :
nothing to replace with
I do apologies but I'm not yet confident in R so I can't understand
how
FILTER
<rle> <iranges> <rle> | <factor> <dnastringset> <dnastringset> <numeric> <character>
[1] chr1 10352 * | NA T TA NA .
[2] chr1 13813-13814 * | NA TT TG NA .
[3] chr1 13813-13814 * | …
updated 19 months ago • Marco
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