txOut=TRUE, dropInfReps=FALSE, varReduce=FALSE)
problem is the output lost the transcript names, just 1,2,3...for row names.
It was fine when I use the following command, without bootstraps
txi <- tximport(files, type="salmon
Order by: Relevance
Given a very simple DNAStringSet, built like this:
afastafile <- DNAStringSet(c("GCAAATGGG", "CCCGGGTT", "AAAGGGTT", "TTTGGGCC"))
names(afastafile) <- c("ABC1\_1", "ABC2\_1", "ABC3\_1", "ABC1\_2")
I would get a DNAStringSetList where the list elements are grouped by a...Given a very simple DNAStringSet, built like this:
afastafile <- DNAStringSet(c("GCAAATGGG", "CCCGGGT…
updated 7.2 years ago • s.ghignone
gr, mcols0$type, mcols0$ID, :
some transcripts have no "transcript_id" attribute ==> their name ("tx_name" column in
the TxDb object) was set to NA
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0...ID, :
the transcript names ("tx_name" column in the TxDb object) imported from the
"transcript_id" attribute are not unique
&…
updated 4.1 years ago • Madza Farias-Virgens
Dear Sir, I am using package"ropls" to generate PCA Plot. I would like to change the labels name to symbol and change the font size of x- and y- axis. In addition, we would like to have the 2 ellipses of vector. How to define
updated 6.5 years ago • laor.cha
Hi,
I am trying to draw a heatmap for my 45 topvar gene by the use of heatmap.2, and when I set a `srtRow=45` in my code(below):
heatmap.2( assay(rld)[ topVarGenes, ], srtRow=45, scale="row",trace="none", dendrogram="column",col = colorRampPalette( rev(brewer.pal(9, "RdBu")) )(255))
row names collided with each other in messy way.
would you please help me to solve this problem? (a…
updated 4.4 years ago • Elham
was hoping to create a new MRexperiment with a subset of the samples. I would like to use the sample name as the feature for which to select the samples by.
I am able to use the: samplesToKeep = which(pData(obj)$sampleName == "XX...create a new MR experiment. but I can only achieve to get one sample at a time using the sample name, so I go from :
_MRexperiment (storageMode: e…
updated 10.4 years ago • rleonzay
set
of
result objects as parameters; but I've got them in a list, and don't
want
to hard-code the names/results. Is there a way to dynamically build
the
parameters as a string and have the string evaluated as such when
calling
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
I checked my design formula it is like this:
ensgeneID as.factor(colData$condition)
1. ESN0000.... control
I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds...I want to have sample names from my summarized experiment (se) in my created DESeqDataSet (dds). I would like to look at the counts data in assay(dds) with...sample names rather than the numeric headers that exist:
> assay(dds)
results …
updated 6.9 years ago • shintzen
<div class="preformatted">Hi list,
I am having trouble with the parameters method in flowCore. When
applying parameters to an element of multipleFilterResult generated by
a tmixFilter, R will throw the following error:
Error in x$parameters : $ operator is invalid for atomic vectors
This came up while trying to apply an other filter to the result of a
tmixFilter.
Best,
Bastian Angermann
…
I am trying to run MAST on a subset of single cell types, but I get the following error:
Error: grouping factors must have > 1 sampled level
Grouping factors are:
```
group ngeneson replicate
neuroblastoma.Bridge -0.791254569558456 jansky...to run MAST on a subset of single cell types, but I get the following error:
Error: grouping factors must have > 1 sampled level
Grouping fact…
me to fix this?
>
> Thanks,
> emily
>
> -- output of sessionInfo():
>
>> names(bedlist)=NULL
>> allorigins=do.call(c, bedlist)
>> allorigins=sort(allorigins)
> Error in x[!nas] : selecting spaces...with 258508 rows and 1 value column across 240 spaces
> space ranges | …
updated 12.6 years ago • Valerie Obenchain
UCSC database.
using the supportedOrganisms() command results in the below error
```Error in names(trackIds) <- sub("^ ", "", nms)```
I have seen previous mentions of this bug having occurred years ago as a consequence of some change...in naming scheme in the UCSC database or something like that, and it was fixed in a later update. Can anyone help me with why I might
updated 22 months ago • thomas
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060321/
f870ecc6/attachment.pl</div
updated 19.8 years ago • mark salsburg
lt;list> <integer> <integer> <integer> <logical> <logical> <character>
1 1,1,1,... 4 114 3251 FALSE FALSE NA
2 T,G,A,... 1 106 2676 FALSE FALSE NA
3 1,1,1,... 6 154 7610 TRUE TRUE …
updated 8.0 years ago • qliu7
Hi all,
Just a quick question regarding a time point experiment I have done. Having asked quite a few questions and read threads I think I have the right design and statistical test for looking for genes that change over time, however, I would just like confirmation if anybody can clarify, what the results output mean as it is concerning me slightly.
I have 10 organs and 4 t…
updated 7.8 years ago • A
I use `` pathfindR `` package and find a problem related to `` pathview `` package.
Error in pathview::pathview(gene.data = gene_data, gene.idtype = "SYMBOL", :
object 'bods' not found
In addition: Warning messages:
1: In run_pathfindR(RA_input, output_dir = "test_dir") :
There already is a directoy named "test_dir". Changing to "test_dir(1)" not to overwrite the pr…
updated 6.5 years ago • Shi-Xiang Wang
Hi all,
When retrieving TCGA data using TCGAbiolinks, I am trying to find from where the column names are sourced and how they are decided e.g.
```r
colData(data)$paper_Telomere.Maintenance
```
or
```r
colData(data)$paper_Survival
updated 2.5 years ago • BioInfoBeginnerrr
<div class="preformatted">Dear list,
I have a set of gpr files that I have read in using read.maimages(),
all of them ending with the number and the date of the experiment.
When I plot the intensities using boxplot() I get the full name of the
sample, i.e. with these long endings. How can I remove these endings?
> data$targets
FileName
slid…
updated 17.5 years ago • darteta001@ikasle.ehu.es
How can I convert entry names such as LYSC_HUMAN into HUGO gene symbols, such as LYZ? UNIPROTKB seems to have another format of identifiers.
```r
head...How can I convert entry names such as LYSC_HUMAN into HUGO gene symbols, such as LYZ? UNIPROTKB seems to have another format of identifiers.
```r
head(keys...Q5TD94" "Q9HA92" "Q9UHA2"
```
These are [accessions][1], whereas I want to c…
updated 4.9 years ago • Dario Strbenac
3084" "23189" "6907" "22866" "55869" "5519" "7314" "471"
so how can i know the full name gene from this R names?
thank you very nutch for any answer
updated 2.8 years ago • chavaleab
div class="preformatted">Hi,
More information about the probe-names problems I'm having with probe
names becoming X12324.at instead of 1234_at
Firstly, this is the version of R I'm using
updated 22.6 years ago • Crispin Miller
KEGGgraph are the entry IDs 12801 and 13489, but what I would like to get are the associated gene names (Cnr1 and Drd2).
I did the following:
library(KEGGgraph)
tmp <- tempfile()
retrieveKGML(pathwayid='mmu04015' , organism='mmu...destfile=tmp, method="wget")
pathway <- parseKGML(tmp)
nodes\[\[60\]\]@name\[\[1\]\] ---> retrieves mmu:12801
nodes\[\[60\]\]@n…
updated 9.9 years ago • Osvaldo
assays = SimpleList(counts = countData), :
the rownames and colnames of the supplied assay(s) must be NULL or
identical to those of the SummarizedExperiment object (or derivative)
to construct
Calls: sourceWithProgress
updated 4.1 years ago • sfpacman
the relevance of Bioconductor
and the BioC2006 conference to the applicant's research.
Applications must be provided on a single page in PDF or RTF
format with indication of name, e-mail address, scholarship track
(student-contributor...developer-contributor, international
student-contributor), text of essay, word count. Applications
must be e-mailed to biocworkshop at fhcrc.org
Applications mu…
updated 19.6 years ago • Vincent J. Carey, Jr.
Hi,
I'm trying to match a `` vector `` of peptide sequences against an `` AAStringSet `` to get all perfect matches.
I thought the most straightforward way to...Hi,
I'm trying to match a `` vector `` of peptide sequences against an `` AAStringSet `` to get all perfect matches.
I thought the most straightforward way to do this is to create a `` PDict `` object from the `` vector `` of…
updated 8.9 years ago • rubi
install("clusterProfiler")
Output:
Error in buildLookupTable(letter_byte_vals, codes) :
vals must be a vector of the length of keys
Error: unable to load R code in package Biostrings
Error: lazy loading failed for package
updated 16 months ago • semra
When attempting to use the compare2sequences tool in CRISPRseek, I received the following error:
--------------------------------------------
> library(CRISPRseek)
> inputFile1Path <- system.file("extdata", "x",
+ package = "CRISPRseek")
> inputFile2Path <- system.file("extdata", "y",
+ package = "CRISPRseek")
> REpatternFil…
updated 9.8 years ago • ragan.pitner
biomart in the "attributes" section, and some of the results are returned with this style chromosome name "CHR\_HSCHR19\_2\_CTG2". How can I correct this?
<pre>
library(biomaRt)</pre>
<pre>
#get annotations for processed transcripts
Is it possible to keep sequence names when haplotypes are collapsed using the Collapse tool of the QSutils package?
I have a number of fasta formatted sequences...gt;Species1", ">Species2", ">Species3" etc. to "1", "2", "3"... I would like to keep the name of at least one of the sequences that have been collapsed together, rather than have them renamed to numbers. Is it possible.…
updated 5.9 years ago • al.gar.aber
output_file=bamname, nthreads = 12)
```
where `fwdname`, `revname`, and `bamname` represent character vectors with 36 elements.
Total alignment time is 16 minutes per sample on average; of these, 5 minutes are spent on
updated 2.5 years ago • Gerhard Thallinger
13 23.66308
This is no problem whatsoever, but help toptable states
"genelist: data frame or character vector containing gene information.
If not specified, this will be taken from the 'genes'
component of 'fit'."
(I hope my
S)<-c("MEST","INHBA","IGF2","H19","GNAS","GRHL1","SNPRN","MEG3","PEG10","CDKN1C")
multiData =vector("list",2)
multiData[[1]] =list(data= R)
multiData[[2]] =list(data= S)
names(multiData)=c("Ref","SGA")
checkSets(multiData, checkStructure...FALSE, useSets = NULL)
multiColor =vector("list",2)
multiColor[[1]] =c('blue',"blue","red","red","grey","tan","tan","purple","grey","purple")
multi…
updated 13 months ago • yang1641
paste, x),])</pre>
I have this error:
<pre>
Error in do.call(paste, resGR) : second argument must be a list</pre>
Perhaps my attempt is not feasible, but it works well if use data.frame. Is there any simple and vectorized
updated 8.9 years ago • Jurat Shahidin
From a character vector of GO IDs (named GOhiIDs containing 142 GO IDs) and I used getAmigoTree and readAmigoDot to get a dot object
updated 10.6 years ago • evepash
gt; GRanges object with 226 ranges and 2 metadata columns:
seqnames ranges strand | name score
<rle> <iranges> <rle> | <character> <numeric>
[1] I 801380 * | peak_C1_H3K4me3_peak_1 4.01076
[2] I 915512 * | peak_C1_H3K4me3_peak_2...seqnames ranges strand | tx_…
updated 3.3 years ago • michela
a bioconductor package) for converting a column of Uniprot IDs to their corresponding protein names using RStudio. But I'm still not able to see the names changing. I'd appreciate it if someone can have a look at my code and...ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
# Get the protein names using biomaRt
search_ids <- c("protein")
protein…
updated 2.8 years ago • a.a.houfani
Error in plotScreen(ldat, zrange = range(mtW), fill = wellCols, nx =
pdim(x)[["ncol"]], : 'fill' must have length >=2 since it is used to
compute the color ramp that represent the values in z.
I think the problem originates...Thanks,
Becky
===========R Console =================
> x <- readPlateList("plateList.txt", name="Automated Preliminary
Analysis", path=dataPath)
A…
got in `` Gviz `` adding an `` AlignmentsTrack `` representing RNA-seq data:
<pre>
Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
negative length vectors are not allowed</pre>
After looking through some code and testing stuff I got...Failure:
tmp <- sequenceLayer(rep(Seq, 700000), rep(Cig, 700000))
Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
negative length ve…
updated 10.1 years ago • Johannes Rainer
div class="preformatted">Hello list
Is there a way to plot chromosome band names along an ideogram using
genome
graphs. I realize that this can be done in quantsmooth but I prefer
the
ideograms generated
updated 14.5 years ago • Pete Shepard
gt; naRatBCv1"),setType=KEGGCollection())
>> illumina.rat.kegg
> GeneSetCollection
> names: 04110, 00400, ..., 00640 (184 total)
> unique identifiers: 2260270, 5900358, ..., 580441 (2557 total)
> types in collection:
> geneIdType...AnnotationIdentifier("illu
mina
> RatBCv1"),setType=GOCollection())
> Error in as.vector(x, "c…
updated 17.6 years ago • Martin Morgan
sam.out, 3, file = "", gene.names =
nrow(data)[[1]],
:
The length of gene.names must be equal to the number of genes.
I know it must be a silly mistake somewhere.. but I'm unable to figure
it
out.
I used a dataset...22622 genes and 40 samples, where the first column
lists
the clone ID ad the second column lists the names, continued with the
rest
40 samples.
With my original data, I gave…
updated 18.6 years ago • Ruma Sanyal
I'm using 64bit R in Windows 10, and my current `memory.limit()` is 16287.
I'm working with mass spectra files (mzXML), I've been calling individual files one at a time using the line below, which
increases my `memory.size()` to 7738.28. Then I filter out noise using basic R functions, and plot the EICs.
msdata <- xcmsRaw(datafile1,profstep=0.01,profmethod="bin",profparam=list…
div class="preformatted">Hello,
In working with HTqPCR lately I noticed that the gene/feature names
are not produced in the output of limmaCtData, even if they are
present in the input. This isn't an issue with ttestCtData...puzzled by how I would annotate multiple
comparisons, so it would definitely be helpful if the gene names
appeared in the output. Unless I'm doing something wrong, but tha…
I . get this error
\`Error in getBM(attributes = c("UniProtKB/Swiss-Prot", "UniProtKB Gene Name", :
Invalid attribute(s): UniProtKB/Swiss-Prot, UniProtKB Gene Name
Please use the function 'listAttributes...to get valid attribute names\`
 
testES) == bks :
comparison (1) is possible only for atomic and list types
I tried making bks a character vector, but to no avail. I also tried
the following:
> testES2 = testES[featureData(testES) %in% bks,] ##(where bks is a
character...vector or not)
Error in testES[featureData(testES) %in% bks, ] :
error in evaluating the argument 'i' in selecting a method for
function...Error …
updated 13.1 years ago • McGee, Monnie
the ROWNAMES and the COLNAMES in the initial numerical matrix/dataframe,
and use identical NAMES (as the ROWNAMES and COLNAMES) in the HeatmapAnnotation() dataframe for precise annotations ?
I am asking the question
updated 8.3 years ago • Bogdan
Hi I am doing the following to get the tximport count matrix with gene name in the first column
<pre>
txdf <- transcripts(EnsDb.Mmusculus.v79, return.type = "DataFrame")
txdf$symbol <- mapIds(EnsDb.Mmusculus.v79
updated 8.2 years ago • tanyabioinfo
Error in DESeqDataSet(se, design = design, ignoreRank) : all variables in design formula must be columns in colData
But the two elements of my design are the two columns in my colData:
```
pData(set_NHP_RUVg)
key_IP_mf.Treatment
s
formulae?
question 2,
for example, I have 5 groups and I want to label each group with a
color name from "#FF0000" to "#0000FF" evenly. so basically i need a
vector like this:
c("#FF0000", ?, ?, ?, "#0000FF")
the number of groups can be 10 or whatever
updated 19.3 years ago • Weiwei Shi
C12","D01","D12",
"E01","F01"))
but get:
Error in checkControls(y = negControls, len = nrChannel, name =
"negControls") :
'negControls' should be a vector of regular expressions with length
1
What's the best way to do this?
Thanks
updated 18.1 years ago • Steve Taylor
extracting information
from a
> "probe.level.object" there is the variables: id , numbers and names.
Is
Do you mean objects of class "Plob" ?
(if yes, what is 'id' ? if no, which class do you refer to ?)
> it correct that probes with "id...has gene name==names[1] - in R
> terms? So that if I for one cell file have called my
>
> > probe.level.object -&a…
rownames(58233): ENSG00000127720 ENSG00000275852 ... ENSG00000119509 ENSG00000200487
rowData names(0):
colnames(313): JUL_0001_rep1_patient1_day3_Flucelvax_Influenza_Male_Age30_batch1
JUL_0001_rep2_patient1_day3_Flucelvax_Influenza_Male_Age30_batch1...JUL_0127_rep3_patient45_day3_Flucelvax_Influenza_Male_Age19_batch12
colData names(21): Unique.ID LongName ... Treatment_Sex_Time sizeFactor
…
updated 8.2 years ago • ap3637
<div class="preformatted">Hello all,
I am trying to repeat a hypergeometric test 40 times by putting it in
a
loop, but I am missing something as it does not work.
How do I substitute a slot name with a string variable?
Here is the code so far:
> probTable <- data.frame(row.names=rownames(repData))
> for (dataset in...by putting it in
a
loop, but I am missing something …
updated 15.5 years ago • Edwin Groot
a quality check of my ATAC-Seq peaks with ChIPQC package but I am getting an error.
```
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
```
So, I need help to solve the...1 3968
> 4 Tumor Twelve 2017 BD033 2 14339
**Error in names(res) <- c…
error message I am getting. My input data includes,
i) myMs - a matrix of M values with feature names (CpG IDs) and sample names
ii) pheno.v - a vector with 0's and 1's describing the 2 unique groups in the data set (cl;ass: numeric...names = group names)
pheno.v
Baseline\_COPD Baseline\_COPD Baseline\_COPD Baseline\_COPD Baseline\_COPD
0 0 0 0 0
Baseline\_COPD
updated 7.7 years ago • poojitha.stemcell
priors are available via the 'type' argument, see ?lfcShrink for details
Error in results(dds.shr, name = coefAlpha, lfcThreshold = lfcThreshold) :
object 'coefAlpha' not found
Calls: lfcShrink -> results
Backtrace:
█
1. └─DESeq2::lfcShrink...dds = dds, res = res)
2. └─DESeq2::results(dds.shr, name = coefAlpha, lfcThreshold = lfcThreshold)
```
It seems like the `co…
updated 6.9 years ago • Michael Steinbaugh
I found that browseGenome in the rtracklayer package fails if the ranges supplied have names. This works:
<pre>
> ir <- IRanges(20000, 50000)
> track <- GRangesForUCSCGenome("hg19", chrom="chr22", ranges=ir)
> browseGenome...with 1 views and 181 tracks
</pre>
This does not work:
<pre>
> ir <- IRanges(20000, 50000, names="a…
updated 10.3 years ago • Stephanie M. Gogarten
to randomly re-order a string
randomizeSeq <- function(mystring){
# split the string into characters
myChars <- unlist(strsplit(as.character(mystring),''))
# randomize the order of characters
random.myChars <- sample...1:4,5,replace=T)], collapse="")
# make a DNAStringSet object
myseqs <- DNAStringSet(c(seq1,seq2))
names(myseqs) <- c("s1", "s2")
# …
loadImages` function from cytomapper.
> dataset
CytoImageList containing 48 image(s)
names(48): 1_A3 1_A4 1_A5 1_A6 1_A7 1_A8 1_B1 1_B2 1_B3 ...
Each image contains 47 channel(s)
channelNames(47): 104Pd_104Pd.ome 113In_113In_HLA...115In_115In_CD11c.ome ...
> display(dataset[[1]])
Error in validImage(x) : object must be an array
> clas…
updated 17 months ago • Dario Strbenac
Recent ...
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