dds <- DESeqDataSet(rse_gene, design = ~some_condition) # some_condition is a random name, it is not in the data.
```
It fails with:
```
Error in DESeqDataSet(rse_gene, design = ~some_condition) :
all variables in design formula...must be columns in colData
```
With a plain counts file, I add this column after loading to the data.frame and everything works
Order by: Relevance
I imported a data as follows which has first column as genes name and other 21 columns for samples with respective counts for genes using >d=read.csv("path/xyz.csv", as.is=T)
THEN, define...this step, I get an error message as follows
<pre>
"Error in .isAllZero(counts) :
count matrix must be integer or double-precision"</pre>
What is the problem as how to solve it ?
&a…
updated 7.8 years ago • Björn
set of mature miRNA counts (un-normalised). I have made the raw counts into a matrix with the row names and column names as the genes and sample name ( they definitely are not part of the matrix). I then have a data frame of the...miRNA_counts[1, ]
miRNA_counts <- miRNA_counts[-1,]
head(miRNA_counts)
# Create genotype vector
Volume <- c("200", "100", "100", "200", "100", …
updated 2.1 years ago • Oenone
<div class="preformatted">
Hi,
I had the same opportunity and ran into the same problem. The error
occurred when trying to read >25 CEL-files with the ReadAffy-package
and
happened in R1.9 as well as R2.0. The problem seemed to be due to an
error
in the Tcl/Tk package and might relate to the installation of Tcl/Tk
on
our Irix machine. We did not completely tracked it down, as we tha…
<div class="preformatted">
Hello dear List,
when I save a cpm table (ordered by p-value for example) , I do not
have the names of the genes but only cpms. How can I add them ?
I used :
> o <- order(lrt$table$PValue)
> tab <- cpm(y)
> write.table(tab, file="CPM.txt...Hello dear List,
when I save a cpm table (ordered by p-value for example) , I do not
have t…
updated 13.2 years ago • Guest User
fgsea, and I keep getting the same error, which I am unable to resolve.
The error is:
"Error in names(res) <- `*vtmp*` :
'names' attribute [30] must be the same length as the vector [20]"
I have already checked a thousand times whether...my ranked genelist has correct, non duplicated, non-missing names, which definitly is the case.
Also have I tried multiple ways of importing th…
updated 3.8 years ago • Barista
at the transcriptomic level. The experiment has the following informations:
## __colData__
<pre>
name cell vector
CellA_1 A vector1
CellB_1 B vector1
... ... ...
CellA_10 A vector10
CellB_10 B vector10
CellA_empty A empty
CellB_empty...B empty</pre>
An empty vector is used as control.
I ran limma-voom and DESeq2 to detect…
updated 10.0 years ago • Radek
at normalization data step and i obtained normalized counts matrix, How can I change Ensemble gene name into common gene name
updated 8.2 years ago • salvocomplicazioni1
21 and base pair position 34203263, but if you go to
Ensembl you will find this snp has a different name rs4591 and the
base pair is 35281393.
I needed to remap all the snps to the current build so I tried biomart...nbsp;filters=c("refsnp"), values=snps, mart=mart)
here is the problem
snps is a vector of rs# from the Affy 6.0 ( there are about 900,000)
snps…
updated 15.7 years ago • Kay Jaja
ERROR
Error in .local(.Object, ...) : allGenes must be a named vector
sessionInfo( )
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura
I'm currently trying to plotting a gene model using ggbio's geom\_alignment() function and I'm interested in annotating the coding sequence (cds) as a thicker part of the track. I'm taking the GRangesList approach described in the into document ( http://www.bioconductor.org/packages/release/bioc/vignettes/ggbio/inst/doc/ggbio.pdf ) section 2.2.4 (page 5).
Here it says …
updated 10.8 years ago • kristoffer.vittingseerup
This isn't a solution to your general question about ..., but
makeContrasts in limma already accepts character vector arguments:
x <- c("a-b","b-c")
makeContrasts(contrasts=x, levels=c("a","b","c"))
Best wishes
Gordon
> Date: Wed, 03 Jun 2009 09
div class="preformatted">Estimated colleagues,
I am working with CGH data. I have the name of the BAC clones and
their
chromosome locations. They correspond to OncoBAC arrays (?).
Is there any way in bioconductor
Hi all, I have a named vector with gene symbols and p-value extracted previously from an Illumina microarray; I'm wondering how to create the...Hi all, I have a named vector with gene symbols and p-value extracted previously from an Illumina microarray; I'm wondering how to create the topgo object with the proper annotation call; so far I have something like this.
glist <- ko\_p…
updated 10.2 years ago • Ahdee
RE: Bioconductor Digest, Vol 68, Issue 23
Dear List,
Is there an elegant way to obtain the name of a probe set from an
Affymetrix platform (doesn't matter which one) corresponding to a
given ENTREZ gene ID? It seems that...are
of
3 types: -1, 1 and 0. 0 means normal probe; -1 mean negative control,
i
guess, and the probe names are like (-)3xSLv1, NC1_00000002, etc[no
corresponding probe sequen…
updated 17.2 years ago • McGee, Monnie
0 rows into table pmfeature... Error in
sqliteExecStatement(con,
statement, bind.data) :
bind.data must have non-zero dimensions
> traceback()
8: stop("bind.data must have non-zero dimensions")
7: sqliteExecStatement(con, statement...like this.
Error in read.xysfiles2(channel1 = file.path(path, files2Ut), channel2
=
file.path(path, :
Must install the pd.100929.hg19.deluxe.prom.meth.h…
updated 12.4 years ago • Nitesh Turaga
the error:
```
`# converting counts to integer mode`
`# some variables in design formula are characters, converting to factorsError in checkFullRank(modelMatrix) : `
`# the model matrix is not full rank, so the model cannot...or interaction terms in the design formula are linear`
`# combinations of the others and must be removed.`
`# Please read the vignette section 'Model matrix …
updated 5.4 years ago • zrf1
a single variant i got pretty confused, from two cases:
CASE 1
> vcf_coding_info_GRanges[names(vcf_coding_info_GRanges) ==
"rs78192809",]
GRanges with 6 ranges and 13 metadata columns:
seqnames ranges strand | paramRangeID...rle> <iranges> <rle> | <factor>
<dnastringset> <iranges> <compressedintegerlist> <…
files with tximport and have transcript level information summarized to gene level (Gene Name). The endpoint is to perform differential expression analysis with either DESeq2 or edgeR.
To this end, I am planning to...provide a tx2gene file in which each transcript points to the corresponding Gene Name.
Is the code below correct?
Please accept my apologies for this basic question, but I am new …
updated 4.5 years ago • luca.s
a count matrix for an RNAseq experiment. I have aligned paired-end .sam files sorted by read name and have specified the -p flag and the −−countReadPairs parameter (please see code below). When I run the command, I get ERROR...if the −−countReadPairs is not included but as I understand it, in version 2.0.2, −−countReadPairs must be included in order to get counts by fragments (as opposed to earli…
updated 4.5 years ago • s.muroy
I tried this code
> exons<-transcriptsBy(txdb,by="gene") [geneVec]
where geneVec is a vector of gene IDs and got this error
Error: subscript contains invalid names
updated 5.2 years ago • pegah.taklifi
contrast=list(CellTypeA, other.CellTypes), listValues = c(1, -1/21))
where other.CellTypes is a vector with the names of all the other 21 cell types.
This works fine. My question is how to set up with same comparison without
updated 5.3 years ago • Kirsty.sawicka
<div class="preformatted">
-----Original Message-----
From: News@bioinformatics.org [mailto:News@bioinformatics.org]
Sent: Thursday, July 29, 2004 2:34 PM
To: Lapointe, David
Subject: [BiO News] Gene name errors introduced by Excel
A research article at BMC Bioinformatics:
BACKGROUND:
When processing microarray data sets...Sent: Thursday, July 29, 2004 2:34 PM
To: Lapointe, David
Subject…
updated 21.4 years ago • David Lapointe
Hi, An error occurred when I used the prePdata function: all (unlist (md_cols)% in% names (md)) is not TRUE:
> sce <- prepData(samp, Panel, Sample_sheet, features = Panel$fcs_colname)
Error in prepData(samp, Panel, Sample_sheet...Hi, An error occurred when I used the prePdata function: all (unlist (md_cols)% in% names (md)) is not TRUE:
> sce <- pr…
updated 2.9 years ago • shuangshuang
extract the data from the
hgu133plus2 package directly.
Something like this (where probids is a vector of probe IDs)
out <- mget(probids, hgu133plus2MAP)
will give you a named list containing the cytoband positions. You
could...turn this into a named vector using unlist(out), and I suppose a
matrix
using cbind(names(out), unlist(out)) but that would be sort of weird
because
updated 20.0 years ago • James W. MacDonald
First,the ensemble-based gtf file that I used to align all my mouse RNAseq data has the chromosomes named as “1, 2 , 3”… Rather than “chr1 , chr2 ..”. My Testing R code for summarizeOverlaps is as follows:
<pre>
library(TxDb.Mmusculus.UCSC.mm10.ensGene...sqlite I am using has chr1, chr2 .. Format
seqinfo(bamLst_grp1) #this shows that the chromosome names for my testing bam …
updated 10.0 years ago • bioprog
mcols0$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
3: In .fin…
T, recursive=FALSE)
tipo<-list()
result_camera<-data.frame("Ngenes"=numeric(),"Direction"=character(),"PValue"=numeric(),"name"=character(),stringsAsFactors = F)
result_mroast<-data.frame("NGenes" =numeric(),"PropDown"=numeric...PropUp"=numeric(),"Direction"=character(),"PValue"=numeric(),
"FDR"=numeric(),"PValue.Mixed"=numeric(), "FDR.Mixed" =num…
Loading required package: reposTools
Loading required package: tools
Error in Bundle(x) : No slot of name "Bundle" for this object of class
"localPck".
I must say that I dearly love the good ship Bioconductor and all who
sail in it
updated 21.1 years ago • michael watson IAH-C
everyone, I am currently getting information of gene type (eg. miRNA, mRNA, lncRNA) from probes name. For example: 1007\_s\_at for a protein-coding gene (mRNA type), 225799\_at for a long non coding RNA (lncRNA). Can some one
updated 8.5 years ago • landscape95
I was running a function:
doCimplAnalysis(data = idata, scales = scale, n\_iterations = 1, BSgenome = Hsapiens, system = "SB", verbose = FALSE)
However, I encountered a error that I am not sure about:
"Error in FUN(X\[\[i\]\], ...) : no slot of name "start" for this object of class "XStringViews" Called from: FU…
updated 9.8 years ago • jbtouching
lt;- mget(ids,KEGGEXTID2PATHID, ifnotfound = NA)
Error in .checkKeysAreWellFormed(keys) :
keys must be supplied in a character vector with no NAs
Can you help? Thanks!
Chen, Yue
________________________________
From: bioconductor...be able to handle all the
other AnnotationDbi. AnnotationDbi packages always end by ".db" in
their name.
To get you started:
# install the package
source("http…
updated 16.0 years ago • Yue, Chen - BMD
elt, sapply, "[[", 1)
vals0 <- lapply(elt, sapply, "[[", 2)
vals <- Map("names<-", vals0, keys)
cols <- unique(unlist(keys))
entries <- Map(function(k) as.vector(sapply(vals, "[", k)),
cols)
desc <- which("DESCRIPTION...toupper(names(entries)))
if (1L == length(desc))
entrie…
updated 11.2 years ago • Anna N.
em></pre>
2. In the author's result file before and after annotation, the probeset column has a name "ID". My result file does not have any name in the first column.
Author's file:
<pre>
<span style="background-color:Yellow...ID <- featureNames(ExpressionSet)
Symbol <- getSYMBOL(ID, "mogene20sttranscriptcluster.db")
Name <- as.c…
updated 11.0 years ago • alakatos
<div class="preformatted">Hi,
I am a Ph.D. student from Quebec, Canada. I'm a beginner with R and
Bioconductor. Until now the only experience I have is in analyzing
microarray data using affy and limma packages. Now I'm trying to
analyze
Rat Gene 10 st arrays and I would like to run RMA analysis and Smyth
moderated t test on those arrays. Since no cdf official package is
available for thos…
updated 16.9 years ago • Anne-Marie Madore
empty keyword value which does not
conform to FCS 3.0 standard:
"3.2.9 Keywords and keyword values must have lengths greater than
zero. "(http://murphylab.cbi.cmu.edu/FCSAPI/FCS3.html).
Particularly, this occurs at $ENDSTEXT...And "\\" is used as delimiter here, FCS 3.0 allows delimiter appears
in the keyword value or keyword name as long as it is " immediately
followed by a second delimiter". S…
na>
miRNA_primary_transcript
score phase ID Alias Name
<numeric> <integer> <character> <characterlist> <character>
[1] <na> <na> MI0022705 MI0022705 hsa-mir-6859-1
[2] <na> <na> MIMAT0027618 MIMAT0027618...hsa-miR-1302
[6] <na> <na> MI0022558…
updated 11.6 years ago • Shraddha Pai
lt; Following Factors in your pd(sample_sheet.csv) will be analysised: >>
<Sample_ID>(character):TCC1, TCC2, TCC3, TCC4, TCC5, TCP1, TCP2, TCP3, TCP4, TCP5, TCP6, TCP7, TCP8, TCP9, TCP10, TCP11
<Sample_Well>(character):A1...B1, C1, D1, E1, F1, G1, H1, A2, B2, C2, D2, E2, F2, G2, H2
<Sample_Group>(character):TCC, TCP
<Slide>…
updated 8.3 years ago • karthikrpad
<div class="preformatted">Dear BioC users,
I am having problems with the getOntology-function (annotate-package
v.
1.18 ) The command
getOntology(getGO( "7650504", "illuminaHumanBCv2")[[1]], "BP" )
[1] "GO:0032515" "GO:0032516"
returns two GO identifiers, but they are not correct since their
ontologies are in fact NA
$`GO:0032515`
$`GO:0032515`$GOID
[1] "GO:0032515"
$`GO:0032515`$Eviden…
y, design);
```
Error:
```
Error in as.vector(x, mode) :
cannot coerce type 'closure' to vector of type 'any'
```
Anyone here that can help me please?
Thanks!
Isabella
lt;-
unique(unlist(as.list(ENTREZIDs[Universe]),use.names=FALSE))
SubjectiveClustersHGT <- vector("list",0)
for(name in names(SubjectiveClusters)){
Temp.Cluster <- SubjectiveClusters[[name]]
Temp.Cluster <- Temp.Cluster...0.01,
conditional = TRUE,
testDirection = "over"
)
cat("HyperGTest for cluster ",name,".\n",sep="")
SubjectiveClustersHGT[[name]] <…
updated 17.6 years ago • Johannes Graumann
GS' at the bottom of the
plot. I would like to use custom row labels for my plot and have
created a vector of names as suggested in the package documentation.
When I try to use this I get the following error:
Error in axis(4, 1:nrow...0, labels =
rnames, :
'at' and 'labels' lengths differ, 52 != 51
suggesting that my rnames vector and the number of rows in the matrix
used for the plot have …
updated 14.4 years ago • Iain Gallagher
quantification, and differentially expressed analysis. Could you teach me how to change sample names, e.g. using Chuong533 instead of Users.gary.Documents.Project.20180429\_ZebraFinchColor.20180508\_Analysis.featurecounts.Chuong553.bam
updated 7.6 years ago • Gary
but I don't know what I doing wrong.
Here my script:
enrichGO(
gene = ortologos_filtrados$Name,
OrgDb = org.Cs.eg.db,
keyType = "ENTREZID",
ont = "MF",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = universe_genes,
qvalueCutoff...minGSSize = 10,
maxGSSize = 500,
readable = FALSE,
pool = FALSE
)
```
I'm using a vector in "gene" …
updated 20 months ago • fernanda.backsouza
goseq on a non-model organism:
I have a set of DE-genes identified by DESeq2 called `` genes ``,
a vector of gene lengths called `` lengthData `` created like this:
<pre>
txdb = makeTxDbFromGFF("../merged_fixed.gtf", format = ("gtf"))
txsByGene...txsByGene))</pre>
And I have a reference set of genes called `` backM `` which is a list of gene names
I am at this point of the gose…
updated 10.0 years ago • Jon Bråte
with the little macro function I wrote to
> perform these normalizations.
These sorts of name collisions can be nasty. There are, however, some
things that package developers can do to make it more difficult for us...pde here=""> users to mess things up.
One of them is for more packages to use name spaces. I believe that
Eric's helper function would not have confused affy if the aff…
error appears:
_"Error in barplot.default(test\_analysis, showCategory = 8) : 'height' must be a vector or a matrix"_
Does anyone know how to save the results from enrichGO in a way that would be possible to use for
updated 7.4 years ago • MAP
There are no adj nodes for node: GO:0010241
Error in switch(type, isa = 0, partof = 1, -1) :
EXPR must be a length 1 vector
I guess that there is something wrong in the annotation packages but
honestly, I might well have misunderstood
updated 15.1 years ago • Johannes Hanson
span>_<span style="background-color:Yellow">Error in XXXX (peakAnnoList) :input object should be a named list (see example below).</span> _However, it all works for test files (provided with ChIPseeker) (see example below)
Any advice...gt; plotAnnoBar(peakAnnoList)
Error in plotAnnoBar(peakAnnoList) :
input object should be a named list...
> plotDistToTSS(peakAnn…
updated 7.8 years ago • k.panov
I get the following error message:
> as("myArrayLM", def);
Error in methodsPackageMetaName("C", name) :
'The name of the object (e.g,. a class or generic function) to
find in the meta-data' must be a single string (got an object of
class
the process correctly):
when I am exporting the csv file, there are duplicate entries for some
gene names (i.e. ESR1). I am under the impression that RMA and the
process I am using (target = 'core') summarizes at the gene level, so
I am...some mouse array data (mouse gene 10 st arrays) and have
not run into this problem of duplicate gene names.
Any insights on what I might be doing incorrectly,…
updated 11.8 years ago • Guest User
not compiled. The CC_score plot is empty.
QCmetrics(tmp2)
> QCmetrics(tmp2)
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", "ReadL", "FragL", :
'names' attribute [9] must be the same length as the vector [7]
ChIPQCreport(tmp2)
> ChIPQCreport...tmp2)
Saving 7 x 7 in image
Error in names(res) <- c("Reads", "Map%", "Filt%", "Dup%", …
updated 6.3 years ago • ryleehackley
and CD8
lymphocyte populations. However, there appears to be no way to give
the second gate a unique name for the workFlow.
I use a quadrantGate to create filters for channels PE.Cy7.A and
PerCP.Cy5.5.A. The quadrantGates...slightly different for the CD4
and CD8 populations (though that does not matter here). The 'action_'
name in the workFlow is different for each one, but the workFlow node
nam…
updated 14.1 years ago • Aric Gregson
find any such
information associated with these objects. I am able to utilise not
only the probe name, but also the x and y positions on the chips too,
but I cannot find a way to associate intensities in the exprset object
to
lumi-package problem: nuID [e.g. nuID2EntrezID()] from vignette example throws an error on my system
I am seeing this:
Error in paste("package", package, sep = ":") :
cannot coerce type 'closure' to vector of type 'character'
I have come across this problem first when I tried to annotate my own
data, but it seems also to happen
gt; Finding all hits in sequence chrUn_gl000249 ...
>>> DONE searching
Building feature vectors for scoring ...
Calculating scores ...
ERROR : replacement has X rows, data has Y</pre>
where X < Y.
Here is the output of sessionInfo...LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
character(0)
other attached…
updated 8.0 years ago • robert_w_link
<div class="preformatted">Dear All,
I am trying to extract the read count from three .bam files. But I am
getting Zero count entries.
I am using Mycobacterium Tuberculosis H37Rv gtf file (
ftp://ftp.ensemblgenomes.org/pub/release-19/bacteria//gtf/bacteria_1_c
ollection/mycobacterium_tuberculosis_h37rv/Mycobacterium_tuberculosis_
h37rv.GCA_000277735.1.19.gtf.gz)
and RNASeq data used here w…
anyone explain what is being used to compute different features within computeFeatures?
I get the naming convention being applied that is spelled out in ?computeFeatures. I don't understand the .0., .a. and .Ba. labels.
For example
updated 11.3 years ago • Max Kuhn
which is the test data set.
Checking samples table... Populating samples table... Error: Column name mismatch.
My environment is Ubuntu 16.04, R 3.4.2, RSQLite 2.0, cummeRbund 2.18.0.
Any one knows
updated 8.1 years ago • zuolin.bai
GeneRegionTrack",chromosome="chr5", genome="hg19",
rstart="exonStarts", rends="exonEnds", gene="name", symbol="name2",
transcript="name", strand="strand", name="RefSeq Genes",
feature="name2",
showId=T, from=122428653, to=122432628)
>...from=122428653, to=122432628)
Error in unit(rep(1, n), "strwidth", data = data) :
'x' and 'units' must have length > 0
> traceback()
12: sto…
updated 13.4 years ago • Winston Timp
Recent ...
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Answer: How to do differential expresion across time serise with edgeR?
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You actually haven't done any DE analysis at all, you've just selected for genes with either zero or large D0 counts.
Another issue is tha…
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