colData)
[1] FALSE
Warning message:
In all(colnames(counts_data)) :
coercing argument of type 'character' to logical
Order by: Relevance
it but got an error:
<pre>
DAVIDQuery(testMe=TRUE)
Error in strsplit(string, "<!--") : non-character argument</pre>
I couldn't find an answer on the Internet so I am asking you here - how can I fix it? I get the same error
updated 10.5 years ago • monicabdimitrova
message (In DESeqDataSet(se, design = design, ignoreRank) :some variables in design formula are characters, converting to factors) which I never encountered in my DESeq2 use before.
My design is already a factor(male and
updated 5.7 years ago • Do it!
EdgeR. However when I have gotten to the steps for path.ids I have noticed that in R it reads as character (empty). I was wondering if anyone knows on why this might happen?
Sincerely,
Ron
updated 9.5 years ago • rl1385
1] NA "1" "1" "1" "1" "NA"
The missing values are in some cases inadvertently recorded as a character string.
 
updated 9.3 years ago • Dario Strbenac
and data analysis skills. Prior experience in genomic research is not essential, but the applicant must be highly motivated to work on problems in medical biology.
The positions will be for 2 years in the first instance. Salary...wehi.edu.au).
Written applications including cover letter, CV and the names of 3 professional referees should be emailed in PDF fo…
This could take some time, please be patient.
All raw data has been loaded.
Error in eval(as.name(names(sort(sapply(X = ls(envir = virtualArray,
pattern = "annot_"), :
error in evaluating the argument 'expr' in selecting a method for...function 'eval': Error in sort.int(x, na.last = na.last, decreasing =
decreasing, ...) :
'x' must be atomic
Is this a bug ?
Greetings,
Robert
-- output …
updated 11.7 years ago • Guest User
catabolic process" has 218 terms in the original but it has 313 terms in the new result ??? This must be due to ENSEMBL database because they both have the same input data files.
Anyone has any advice/suggestion?
 ...nbsp; genelist<-factor(as.integer(geneuniverse %in% geneofinterest))
names(genelist)<-geneuniverse
 …
package, it seems like the model for q\_ij is:
q\_ij = exp(x^T \* beta)
where x is the vector of covariates and beta the vector of coefficients in glm negative binomial model.
It seems like if we only have 1 factor
updated 9.9 years ago • lanhuong
<div class="preformatted">Sorry to keep posting this, I am very new user of Bioconductor and I
cant
seem to find any clarification on this anywhere.. This is somewhat
related
to this question listed below, I just want some more clarification on
using
the CNA function. This is probably very elementary, I apologize in
advance
https://stat.ethz.ch/pipermail/bioconductor/2007-September/019138.…
bindingIsLocked(m1, where) : not an environment
Error in setClass("graphNEL", representation(nodes = "vector", edgeL =
"list"),
:
Error in contained classes ("graph") for class "graphNEL";
class definition removed from "graph"
[1] FALSE
Loading...bindingIsLocked(m1, where) : not an environment
Error in setClass("graphNEL", representation(nodes = "vector", edgeL =
"list"),
:
Erro…
Hey, I have the circular Ecoli genome, and I want to construct a GRanges object of all ORFs in the fasta file from ncbi.
I made a c++ function to do it, but of course since some of the orfs that starts just before the stop of the genome, and ends after the start, will make IRanges() constructor output error (negative widths not allowed), I want to something like in R where you can se…
C:/rfiles/koolfile",full.names=TRUE)
> rawdata=ReadAffy(filenames=fns2)
Error: cannot allocate vector of size 640.9 Mb
In addition: Warning messages:
1: In dimnames(x) <- dn :
Reached total allocation of 1021Mb: see help(memory.size...gt; memory.limit(size=4095)
[1] 4095
> rawdata=ReadAffy(filenames=fns2)
Error: cannot allocate vector of size 640.9 Mb
[[alternative…
updated 15.8 years ago • sneha patil
padj symbol
<numeric> <numeric> <numeric> <numeric> <numeric> <numeric> <character>
ENSG00000100053 1.851747 -17.2457 3.50063 -4.76078 1.92847e-06 8.94392e-03 CRYBB3
ENSG00000112473 371.466157...16.6164 3.44713 -4.65212 3.28545e-06 1.20989e-02 ARHGAP11B
entrez
…
updated 5.4 years ago • anthony.nash
Broad Institute Release 3</code>
followed the example in the tutorial, constructed the DE genes vector:
<pre>
> genes
ENSFCAG00000015719
1
ENSFCAG00000005390
0
…</pre>
then calculated pwf:
<pre>
> pwf=nullp(genes,"felCat5","ensGene...there is no package called ‘NA.db’</pre>
As a novice R user, …
updated 10.4 years ago • xyliu00
Hi, I recently upgraded to latest **R 4.3** from **R 4.1**. While running the DEA workflow on scRNA-seq data, I noticed it was dramatically slower with my latest setup. I wonder if anyone are aware of changes that may have contributed to this, and how I can make the dispersion estimation step to run as fast as before?
Using a small dataset with 49 cells as demo (22 vs. 27 in two tissues), here'…
path="C:\\Playground\\Micro")
>
> #This is the object
>> target
> SlideNumber Name FileName Cy3 Cy5
> array1 1 c1 array1.xls control treatment
> array2 2 c2 array2.xls control treatment
>
> #and how...quantarray = { : could not find function
"readBlueFuseHeader"
>
> #I've also t…
the block, then
it would have.
It is possible with a little R programming to expand out your data
vector stuff$Rb[,1] to be the
right length by adding NAs in the right places, so that you could use
imageplot(), but this bit of
code...targets$FileName,source="agilent")
>> #Setup layout
>> stuff$genes$Block <- 1
>> names(stuff$genes)[2] <- "C…
package.
I
don't have any other statistics for these genes. Is it possible to
carry
out GSEA on a vector of Entrezids which is ordered by say fold change?
I
attach an example vector and would like to carry out GSEA on this test...unique(getEG(sample(ls(hgu95av2GO), 100), "hgu95av2"))
set1<-na.omit(set1) # as I get NAs in the vector before
For GSEA I assume that element set1[1] has highest…
updated 17.5 years ago • Chanchal Kumar
aln <- readAligned("data",type="SolexaExport",pattern="*.txt.gz")
## free some mem!
gc()
## the names are different from what we expect (UCSC standards), as
they have an additional .fa extension
levels(chromosome(aln)) ## faster...have seen
when you want to use biomaRt as an annotation source
## for this easyRNASeq requires the name of the organism, which
circumvent the "custom" chromoso…
updated 13.9 years ago • delhomme@embl.de
Does sampleNames(ABatch) do what you want?
Best,
Jim
D.Enrique ESCOBAR ESPINOZA wrote:
> Hi,
> i want to fetch filename in an AffyBatch object,
> I don t know how to do it,
> when i do:
> =====================
> for (i in seq(1:ncol(exprs(ABatch_RawD)))){
> print(paste("i=",i,sep=""))
> print(pData(ABatch_RawD[,i])[1])
> }
> =========…
updated 19.1 years ago • James W. MacDonald
Hello, I have googled my self half to death, I cannot understand this:
select(hta20transcriptcluster.db, keys=featureNames(vv), columns=c("SYMBOL","GENENAME"), keytype="Ensemble")
Error in testForValidKeytype(x, keytype) :
Invalid keytype: Ensemble. Please use the keytypes method to see a listing of valid arguments.
My probes look like this:
\[997\] "TC01000131…
updated 7.0 years ago • Pindre
Hi,
i want to fetch filename in an AffyBatch object,
I don t know how to do it,
when i do:
=====================
for (i in seq(1:ncol(exprs(ABatch_RawD)))){
print(paste("i=",i,sep=""))
print(pData(ABatch_RawD[,i])[1])
}
=====================
it returns:
>>>>>>>>>>>>>>>>>>>>>>
[1] "i=1"
…
updated 19.1 years ago • D.Enrique ESCOBAR ESPINOZA
case the function extractCoords doesn't report a data frame with coordinates, as it should, but a character vector instead.
What about something like?:
<code>extractCoords <- function(xx)<br/>
{<br/>
coords <- sapply(xx, strsplit
updated 9.0 years ago • Xavier Pastor
normalize\_seqnames\_replacement\_value(value, x) :
\#\# levels of supplied 'seqnames' must be identical to 'seqlevels(x)'__
GenomicRanges:::.normalize\_seqnames\_replacement\_value
\#\# function (value, x)
\#\# {
\#\#  ...levels(value), seqlevels(x)))
\#\# stop("levels of supplied 'seqnames' must be ",…
updated 9.2 years ago • wcstcyx
the following error in GENESIS?
```r
Error in crossprod(x, y): requires numeric/complex matrix/vector arguments
updated 23 months ago • Stephanie M. Gogarten
filename="master_DE_list.txt", method="union", lfc_filter=TRUE)
Error in (function (cl, name, valueClass) :
assignment of an object of class “NULL” is not valid for @‘allNames’ in an object of class “DESeqResMeta”; is(value...character") is not TRUE
```
I have tried to replace the NA data points in my data to zeros using the is.na() <- 0 function, but then I get
updated 3.6 years ago • Ana
ExpressionSet (storageMode: lockedEnvironment)
assayData: 54675 features, 214 samples
element names: exprs, se.exprs
phenoData
rowNames:
[...]
> class(pd)
[1] "data.frame"
> pData(da.rma) <- pd
> results <- pairwise.comparison...for slot
> "members" in class "PairComp": got class "numeric", should be or
> extend class "character"
> …
updated 17.5 years ago • David Ruau
NA 24655
I did the following for the entire genome
gal <- readBamFile(bamfile, tag=character(0),asMates=TRUE, bigFile=TRUE)
shiftedBamfile <- file.path(outPath, "shifted.bam")
gal1 <- shiftGAlignmentsList...100),
param = ScanBamParam(tag=possibleTag))[[1]]$tag
tags <- names(bamTop100)[lengths(bamTop100)==100]
t…
Il10 ko",
+ annot = annFUN.hgu,
+ affyLib = affyLib)
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class "AsIs" is not valid for
slot
"allGenes" in an object of class "topGOdata"; is(value,
"character
sample_meta$sampleID)
sample_meta$Group <- as.factor(sample_meta$Group)
sample_meta$Name <- as.factor(sample_meta$Name)
#get the clusterID from fSOM object
clusterID <- as.factor(fSOM$FlowSOM$map$mapping[,1...levels(clusterID) <- fSOM$metaclustering
#I need to have a list of "file name" "from" "to". The original one from here ht…
Dear Gordon and all,
I'm analyzing Illumina 450K methylation data with following study design:
Study design: I have individuals at a given time-point from three different stages: Stage 1, 2 and 3 and I wish to identify differentially methylated CpGs in these groups. Stage 1 vs Stage 2; Stage 1 vs Stage 3 and Stage 2 vs Stage 3
I have preprocessed my data and adjusted for batch effect…
updated 9.2 years ago • DSP
which
offers
completely redefined probesets but again
you will lose many probes.
I think there must be people around, who analyze these arrays quite
frequently and must have more insight. So I wondered if a standard
procedure
bit different with the two different covariate, 'time' and 'timen'.
btw: what type of "reps" is it? character or numeric? I loaded it as the character, I don't know if it is ok when doing analysing.
thanks!
 
updated 7.8 years ago • yadongxue
strand | RefSNP_id alleles_as_ambig
<Rle> <integer> <Rle> | <character> <character>
[1] 13 31872705 * | rs3 Y
-------
seqinfo: 25 sequences (1 circular) from GRCh38.p7 genome
What is the recommended
updated 7.9 years ago • sandmann.t
stored in the exprs slot of PAcalls
>PAcalls <- mas5calls(raw.data)
>
># This returns a vector where each probeset is listed with the total
>number of present calls
>np <- number.pres(PAcalls@exprs)
>
># Get...those probesets with at least 1 present call
>my.list <- names(np[np>0])
>
>The simpleaffy …
updated 21.0 years ago • Naomi Altman
I am receiving an error that "row names of the colData are not the same as in the countData. But I can't find any discrepancy.
thank you
> count
updated 7.1 years ago • lara
nbsp; bamFile sequencingPrimer
<character> <factor> <numeric> <character>  ...nbsp; <character&…
updated 10.1 years ago • dzis
winSize =
250)
Smoothing Chromosome 21 ...
Note: Method with signature âGenoSet#character#ANY#ANYâ chosen for
function â[â,
target signature âMethyGenoSet#character#character#missingâ.
"MethyGenoSet
data = "logcounts",assay = 'RNA',project = 'SingleCellExperiment')
Warning: Non-unique cell names (colnames) present in the input matrix, making unique
Warning: Feature names cannot have underscores ('_'), replacing with...dashes ('-')
Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-')
Error in intI(j, n = d[2], dn[[2]], give.dn = FALSE) :
invalid character …
updated 4.7 years ago • rohitsatyam102
if try
to query it by gene-id.
pathways <- try(get.pathways.by.genes(c("mtu:Rv2702")))
pathways
character(0)
Anybody has an idea why this happens?
Thanks in advance,
Naha
[[alternative HTML version deleted]]
</div
updated 14.5 years ago • Naharajan Lakshmanaperumal
div class="preformatted">I have the following object (summary of tukeyHSD). How can i retrieve
the characters "S-H" "SI-H" and "SI-S"
I though that tuk.dat$disease[x,] would do it but is not, neither
tuk.dat$disease[[x]]
Can you help me ?
str
updated 15.5 years ago • David
cooks
rownames(65988): ENSG00000000003 ENSG00000000005 ... ENSG00000282821 ENSG00000282822
rowData names(21): baseMean baseVar ... deviance maxCooks
colnames(12): c1 c2 ... m5 m6
colData names(2): condition sizeFactor
Hers:
> dds
class...ENSG00000000003 ENSG00000000005 ... ENSG00000282821 ENSG00000282822
rowRanges metadata column names(27): baseMean baseVar ... deviance maxCook…
updated 8.6 years ago • dmffrancisco91
The featureCounts manuscript mentions that for RNA-Seq multi-overlapping reads must not be counted and the reasoning seems logical.
> We recommend that reads or fragments overlapping more than one gene...gt; are not counted for RNA-seq experiments because any single fragment
> must originate from only one of the target genes but the identity of
> the true target gene cannot …
updated 11 months ago • Arindam
<div class="preformatted">Can one put more than one vector in the ColSideColors option, so
heatmap,
like dChip, can color the columns using different grouping labels?
Thanks,
...Tao...div class="preformatted">Can one put more than one vector in the ColSideColors option, so
heatmap,
like dChip, can color the columns using different grouping labels?
Thanks
updated 21.9 years ago • Shi, Tao
Hi Matt, and BioCs
I am about to start an analysis of a manually curated dataset built
upon ~80 GDS's (Mouse 430 2.0 platform)
I wonder if there are plans to support that platform in near-future
releases of frma.
Thanks in advance
Ariel./
Dr. Ariel Chernomoretz
Integrative Systems Biology Group
Fundacion Instituto Leloir
Ave. Patricias Argentinas 435
C1405BWE Buenos Aires
Argentina
TRUE)
## Warning messages:
## 1: In asMethod(object) :
## sparse->dense coercion: allocating vector of size 11.7 GiB
sce2 <- cxds_bcds_hybrid(sce2, estNdbl = TRUE)
## Setting levels: control = 0, case = 1
## Setting direction: controls...match of 'prob' to 'probs'
## 4: In asMethod(object) :
## sparse->dense coercion: allocating vector of size 11.7 GiB
```
Is …
updated 19 months ago • Lluís Revilla Sancho
<div class="preformatted">Dear all,
First, I would like to thank S. Falcon, J.W. MacDonald and J. Zhang
for
their
help on my previous questions.
I want to use the function hyperGTest on arabidopsis data, but it
seems
that there is a little bug
in this function. This is an example that gives me an error message
(hereafter, allegenes is a vector
of selected genes)
genesel<-c("AT1G55…
gt; MTP(X=t(as.matrix(x)), Y=y, test="lm.YvsXZ", B=NumPermutations)
Where x and y are two numerical vectors. In Comparison: The standard
"lm"
function does compute a pvalue for these two vectors.
Best regards,
Benjamin Otto
======================================
Benjamin
updated 18.5 years ago • Benjamin Otto
<div class="preformatted">Hi John,
I am having trouble reproducing this. Can you please send me your
"ilmn_cust_raw.txt" file along with the sessionInfo() when you built
your package?
Marc
John Lande wrote:
> dear All,
>
> I am trying to build an annotation package with annotationDbi. I
followed
> the instruction to build the package, with this script:
&…
updated 16.0 years ago • Marc Carlson
<div class="preformatted">Dear all,
I have been trying to use the topGO package to identify over-
represented
GO terms in a specific list of genes. The list does not come out of a
micro-array analysis and I have therefore tried to built a "topGOdata"
object through the following procedure :
sampleGOdata <- new("topGOdata", ontology = "BP", allGenes =
MygeneList,
annot = annFUN.gene…
<div class="preformatted">---------- Forwarded message ----------
From: stephen sefick <ssefick@gmail.com>
Date: Wed, Feb 3, 2010 at 11:31 PM
Subject: modifyWeights Problem
To: bioc-devel at stat.math.ethz.ch
I am using the limma packages for the first time, and I need help with
the modifyWeights function. ?I have about three years of experience
with R programing, but this is the fir…
<div class="preformatted">Dear All,
we update our R installation via a cron job, but it fails with
Error in eval(expr, envir, enclos) :
You have an outdated biocLite() function. Run 'rm(biocLite)' and try
again.
Calls: source ... local -> eval.parent -> eval -> eval -> eval -> eval
Execution halted
If the commands are run directly in R or the cron s…
updated 14.0 years ago • Iain Morrison
ranges strand | exon_id exon_name
exon_rank
<rle> <iranges> <rle> | <integer> <character>
<integer>
[1] chr1 [66999065, 66999090] + | 1 <na>
1
[2] chr1 [66999928, 67000051] + | 2 <na>
2
[3] chr1 [67091529, 67091593] + | 3 <na>
3
[4] …
updated 13.7 years ago • Halian Vilela
fdef, mtable) :
unable to find an inherited method for function ‘assay’ for signature ‘"matrix", "character"’
```
error is not showing with calculateSumFactors please suggest me why this error I am getting in case of computeSumFactors
KEGGSOAP package.
E.g. reactions <-get.reactions.by.pathway("path:hsa05416" ) gives me
output character(0)
while for example
genes <-get.genes.by.pathway("path:hsa05416" ) works fine giving the
list of gene identifiers
updated 13.1 years ago • Marinkovic Tijana
mtable) :
unable to find an inherited method for function "rowttests", for
signature "matrix", "character"
Appreciate any kind help. Thanks.
Xin
</div
updated 17.7 years ago • Xin Zheng
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."
it has happened twice
updated 5.9 years ago • ross.kedl
gt; y <- DGEList(counts=rawdata[,4:9], genes=rawdata[,1:3])
## Error in colSums(counts) : 'x' must be numeric
object: invalid
object
for slot "srcUrl" in class "GO": got class "list", should be or extend
class "character"
> mode(urlData[["GO"]])
[1] "character"
> class(urlData[["GO"]])
[1] "character"
> urlData[["GO"]]
[1] "http://sioux.fhcrc.org/MIRROR archive.godatabase.org
updated 20.2 years ago • Denise Mauldin
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ja569116
•
0
Hi @atpoint Thanks for the information.
Could you please expand on when to use adjusted p-values vs nominal p-values.
My understanding was …
Answer: limpa analysis advice
by
Gordon Smyth
53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma
by
Gordon Smyth
53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry
by
Gordon Smyth
53k
I updated the above answer today.
Answer: When to use edgeR or limma
by
James W. MacDonald
68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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