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 way to do it?
I also put this question in bioconductor since I believe
Order by: Relevance
other.
To avoid this issue, I wished to plot only a few custom genes filtered based on the gene name. The key question is how would I do that in such a way that Txdb object makes its own filtered Txdb object which then I can...genes[gene.data$genes$gene_id %in% ranges.df[ranges.df$coverage == unique(ranges.df$coverage)[1],]$names]
```
2. select() won't work here, but can I make it a custom T…
updated 2.6 years ago • Shreyash
block:
```r
> TPC_group=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test.h5",name='/TPC_tables')
> head(t(TPC_group$'29'))
[,1] [,2] [,3] [,4] [,5]
[1,] 0.52002 -69.81251 0 -0.04637020 0.007849086
[2,] 0.52004 -69.81251 0 -0.04497140...0.149694873
> TPC=h5read(file="/Users/julienballbe/Downloads/New_cell_file_full_test…
updated 3.0 years ago • julien.ballbe
div class="preformatted">
Is there a way for me to use Bioconductor to take a list of gene names
and give me back a list of genomic sequences, preferably with the
exons and introns easily differentiable (e.g. exons
updated 12.5 years ago • Guest User
to adapt
code written for Agilent single channel data, is how to
'automatically' include gene names, symbols, GO IDs etc in the
topTable output. While it may be easy enough to use mget to retrieve
the necessary info for small...is what I have done so far.
Since there is such a rich repository of data in hgu133plus2.db, there
must be a way to tap into this without going 'outside' limma. Can
anyon…
updated 14.8 years ago • David Iles
I want to split into multiple BAM files, based on the "_tags_" that I have appended in the read names (so __qname__ param) . I thought it might be possible using \``` Rsamtools::filterBam() ``\` function if I am able to provide the...expect a single DataFrame argument representing all information specified by param. Each function must return a logical vector, usually of length equal to …
updated 9.9 years ago • Vivek.b
between different groups
(this
is not array data and i'm not using limma). Any on what the error must
be ?
> mydata.eset
ExpressionSet (storageMode: lockedEnvironment)
assayData: 2754598 features, 3 samples
element names
updated 14.9 years ago • David
Hi, I'm trying to change the font size of the gene name and increase the arrow head size.
I've tried changing the cex and cex.id but it does'nt seem to be effecting the font size...Hi, I'm trying to change the font size of the gene name and increase the arrow head size.
I've tried changing the cex and cex.id but it does'nt seem to be effecting the font size; for example below I set both to 30 w…
EBTest(Data = ebvRna1, Conditions = condition1, sizeFactors = sizes, :
Please add gene/isoform names to the data matrix**
But I checked my Data by
**str(ebvRna1)**
**int [1:395, 1:20531] 2 2 2 2 2 2 2 2 2 2 ...
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:20531...LOC100130426" "UBE2Q2P3" "UBE2Q2P3.1" "LOC149767" ...**
It looks I have the gene names for my matrix. Doe…
updated 5.5 years ago • lli2
in validObject(.Object) : invalid class "GRanges" object: 'seqlevels(seqinfo(x))' and 'levels(seqnames(x))' are not identical\`
However, all intersection objects are (gr12, gr13 and gr23) are valid (tested by e.g. \`validObject
updated 9.3 years ago • WouterDeCoster
set IDs. This is after normalisation and linear model fitting.
However when I try to apply gene names the error below occurs.
Error in text.default(fit$coef[topGenes],fit$lods[topGenes],
labels=substring(genelist[topGenes...labels'
The volcano plot is produced but with no labels. Also the TopTable
does not contain gene names or functions. This occurs with data files
from two different chips.…
Warning messages:
1: In maximumLevels(fac, n = length(colors)) :
A factor was provided with 16 levels, but the colour map used here has only 9 colours. For the purpose of colouring, levels 9 ('complete solution minus iron, Kas...1, complete solution, 24 hour') are being collapsed. Please consider grouping together some of the levels of your factor of interest to reduce the number of levels, t…
updated 9.9 years ago • Maria Keays
genomdat)) genomdat <- as.matrix(genomdat)
if (!is.numeric(genomdat)) stop("genomdat must be numeric")
if (!is.numeric(maploc)) stop("maploc must be numeric")
data.type <- match.arg(data.type)
ina <- (!is.na(chrom) &...length(sampleid) != ncol(genomdat)) {
warning("length(sampleid) and ncol(genomdat) differ, names ignored\n")
…
updated 5.0 years ago • El
lapply(package, packageDescription, encoding = NA)
if (length(package) == 0)
stop("no valid packages were specified")
basePkgs <- sapply(pkgDesc, function(x) !is.null(x$Priority) &&
x$Priority == "base")
z$basePkgs...lt;- package[basePkgs]
if (any(!basePkgs)) {
z$otherPkgs <- pkgDesc[!basePkgs]
names(z$otherPkgs) &l…
doc/tximport.html) shows two ways to import results for differential expression analysis at the gene level.
The first approach (used with DESeq and edgeR) is to use the estimated counts from your quantification tool of choice
for temp files : . ||
|| Threads : 8 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : not counted ||
|| M…
updated 3.8 years ago • Zhaoxu
Hello,
I am analysing RNA-seq data to find differentially expressed genes between a wild-type (Ctl) and mutant (Mut). The mutant has a large DNA duplication encompassing several hundred genes, so they always come up as ~2x upregulated but this is not biologically interesting. Hence the H0 (null) for these particular genes is that Mut = 2 x Ctl, while H0 for the rest of the genes is Mut = Ctl.
M…
updated 9.9 years ago • stuart
8 7 9 7 8
244973 4 3 2 6 7
244973 8 5 3 6 8
I would like to extract only the probe names and tried this:
degtl - original matrix( containing 22810 entries)
ids <- degtl[,1]
and I got
head(ids)
[1] 244941_at 244959_s_at...244974_at 245009_at 245024_at
245028_at
22810 Levels: 244901_at 244902_at 244903_at 244904_at 244905_at
244906_at 244907_at 244908_at ... AFFX-TrpnX…
cnames[2])</pre>
I am very puzzled why `` procset ```` () `` requires exactly one column name. This totally doesn't make sense. In addition, it is very slow for my dataset (19000 single cells). I would like to improve speed...78). For that, I need to know why `` procset ```` () `` requires exactly one column name and whether I can remove this condition.
…
updated 7.8 years ago • klv2706w
I have some bam files with chromosome names like "1" instead of "chr1". I run into problems when I want to plot data from ensembl along with coverage data from these bam...to modify the function that reads data from the bam file somehow so that it returns the chromosome name prefixed with "chr". Is that possible? I tried editing the default import function, only editing the line giving seqnames
updated 8.9 years ago • stianlagstad
name is
deprecated)
read_maq_map.cc:150: error: there are no arguments to
'new_XStringSet_from_RoSeqs' that depend on a template...parameter, so a
declaration of 'new_XStringSet_from_RoSeqs' must be available
read_maq_map.cc:151: error: there are no arguments to
'new_RoSeqs_from_CharAEAE' that depend on a template...parameter, so a
declaration of 'new_RoSeqs_from_CharAEAE' must be available
read_…
Dear experts,
Given the accession IDs such as these:
How can I extract the "chromosome name", "start" and "end" position
of each ID, with BioConductor.
AB002292
AB002296
AB002298
AB002303
..
EF565109
K03493
L36149
M16404
updated 17.2 years ago • Gundala Viswanath
T)
\#\[1\] 8471
I did the same comparison (A vs. B) by removing the factors "C" and "D" from the level which resulted in 7221 differential expressed genes.
\# remove the levels C and D
dds\_sub <- dds\[, dds$condition %in% c("A", "B")\]
dds
updated 11.2 years ago • mat.lesche
is to share information (dispersion estimates) across genes with similar average expression levels. This is under the assumption that genes with similar expression levels should have similar dispersions and are thus...subject to shrinkage once a curve is fitted that represent an accurate estimate for dispersion levels. The larger a dispersion value, the larger the difference in expression has to …
with 258508 rows and 1 value column across 240 spaces
> space ranges | name
> <factor> <iranges> | <character>
> 1 chr1 [ 564401, 570399] | 2726
> 2 chr1 [ 756001, 758799] | 76
> 3 chr1 [ 811201, 811799] | 34
> 4 …
updated 12.6 years ago • Valerie Obenchain
genome. It seems
like bigwig saved with the official NCBI/Ensembl/flybase mitochorion
chromosome name dmel_mitochondrion_genome breaks the importation of a
previously saved files (which does not break when loaded in...other
tools like the Broad IGV). Changing the chromosome name to something
smaller fixes the issues. Is that a bug or its per design
Look like a bug to me
Heres a sample script …
updated 11.5 years ago • Marco Blanchette
Hello,
I want to add gene names to rlog transformation for heatmap, I'm trying to install Biomart but I have some problems with.
So I'm asking for another
updated 6.7 years ago • saida3112
Gene_Type Gene_Name MGI_ID
1 chr1 HAVANA gene 3073253 3074322 + level 2 ENSMUSG00000102693 TEC 4933401J01Rik MGI:1918292
2 chr1 ENSEMBL gene 3102016 3102125 + level 3 ENSMUSG00000064842...snRNA Gm26206 MGI:5455983
3 chr1 HAVANA gene 3205901 3671498 - level 2 ENSMUSG00000051951 …
updated 5.3 years ago • anjali_mohan
I'm trying to import some salmon quant.sf files and convert them to gene level TPMs with `tximport`.
I have checked whether the files exist, and all files do.
All these files have a long "transcript name...counts
summarizing length
Error in rowsum.default(x[sub.idx, , drop = FALSE], geneId) :
'x' must be numeric
```
I tried importing the same files with `map` and `read_tsv` while bin…
updated 4.8 years ago • Ezgi
col.histogram = "darkblue",
fill.histogram = "darkblue", ylim = c(-.5,
4),
name = "Conservation")
I receive the following error:
Error in makeNewSeqnames(x, new2old = new2old, seqlevels(value)) :
when 'new2old...is NULL, the first elements in the
supplied 'seqlevels' must be identical to 'seqlevels(x)'
> traceback()
9: stop("when '…
updated 12.6 years ago • Guest User
FALSE, stringsAsFactors=FALSE)
> rn<-paste(data[,1], sep="")
> P_values=data[,-1]
> names(P_values)<-rn
> myGOdata=P_values
> relevant.genes <- factor(as.integer(all.genes %in% myGOdata)
+ )
> names(relevant.genes...There are no adj nodes for node: GO:1905313
Error in switch(type, isa = 0, partof = 1, -1) :
EXPR must be a le…
updated 8.9 years ago • hollinew
tried to create count matrix I used "summarizeOverlaps" of "GenomicAlignments". I always sort BAM by name before this step. But I am now wondering if it's necessary as I haven't see any instruction on this part. I did ask the similar
updated 10.4 years ago • Xiaokuan Wei
cg00446235" "cg00563845" "cg00955230"
How do I convert these ID's into the standard gene names/symbols in R?
Thanks
updated 7.5 years ago • arbet003
but I'm having problems,
i'm
getting this error message:
Error in apply(dat, 2, mode) : dim(X) must have a positive length
The files that I'm using to test are:
sample_info_file:
Array name Sample Name Batch
array1 sample1_cy3
updated 12.8 years ago • Edwin
packages and got problems running TCGAanalyze_DEA of TCGAbiolinks with the following error "Error in names(x) <- value :
'names' attribute [7] must be the same length as the vector [5]". No error was reported till the TCGAanalyze_DEA functions
updated 6.2 years ago • messimess
under R 1.9.0
and Bioconductor v1.4:
?Error in boxplot.default(yy ~ xx, xlab = "PrintTip", ylab = "M",
names = c("(1,1)", :
names attribute [16] must be the same length as the vector
[1]?
The exact same test code works fine under R 1.8.1 (? and whatever
updated 21.5 years ago • White, Charles E WRAIR-Wash DC
be great\]:
1) providing a Data package (let's call it MTseekerData, because that's its name) holding data structures where
2) the S4 class data structures are generated from a package (let's call it MTseeker, because...that's its name), and
3) the package (MTseeker) requires the MTseekerData package and the latter must be submitted as a GitHub issue
updated 7.2 years ago • Tim Triche
expressions.tsv",sep="\t",stringsAsFactors=F)
rownames(eset) <- eset[,1]
eset <- eset[,-1]
names(eset) <- gsub("^X","",names(eset))
samples <- read.delim("mySamples.tsv",sep="\t",stringsAsFactors=F)
TS <- factor(samples$Condition...levels=unique(samples$Condition))
design <- model.matrix(~0 + TS)
colnames(design) <- levels(TS)
cont.matrix <-…
It looks fine until the step
> dds <- DESeq(dds)
estimating size factors
Error in .Call(.NAME, ..., PACKAGE = PACKAGE) :
Incorrect number of arguments (6), expecting 4 for 'select_hits'.
A while ago, I ran another DESeq2 script
Order, function(x) max(x))
x = sort(x, TRUE)
sigtab$Order = factor(as.character(sigtab$Order), levels=names(x))
\# Genus order
x = tapply(sigtab$log2FoldChange, sigtab$Genus, function(x) max(x))
x = sort(x, TRUE)
sigtab$Genus = factor(as.character...sigtab$Genus), levels=names(x))
ggplot(sigtab, aes(x=Genus, y=log2FoldChange, color=Order)) + geom\_point(size=6) +
theme(axis.text.x = eleme…
TTGAAA-CTC-N
> DNAString("TTGAAA-CTC-N", "A")
Error in .normargSEW(start, "start") :
'start' must be a vector of integers
> DNAString("TTGAAA-CTC-N", "A", "B")
Error in .normargSEW(start, "start") :
'start' must be a vector of integers...bases)
*** caught segfault ***
address 0x1, cause 'memory not mapped'
Traceback:
1: .Call(.NAME, ..., PACKAGE = PACKAGE)
2: .Cal…
updated 7.8 years ago • ebiederstedt
min.sz=10,
max.sz=500, verbose=TRUE)$es.obs
Mapping identifiers between gene sets and feature names
|
| 0%)
The process has forked and you cannot use this CoreFoundation
functionality safely. You MUST exec().
Break on __THE_PROCESS_HAS_FORKED_AND_YOU_CANNOT_USE_THIS_COREFOUNDATI...to debug.
....etcetcetc. The process hangs here.
I get the same messages with my own data. I must have overloo…
required to perform 'background
correction', but from some later point in the analysis that you must
determine (because the data has likely already had some kinds of data
transformation applied).
Background correction
updated 17.9 years ago • Martin Morgan
the conference proceedings to both EI and ISTP for indexing.
ICNC'09-FSKD'09 aims to provide a high-level international forum for
scientists and researchers to present the state of the art of
intelligent methods inspired...are encouraged to propose invited sessions. The first author
of each paper in an invited session must not be affiliated with an
organization in China. All papers in the invite…
updated 16.8 years ago • ICNC'09-FSKD'09
the conference proceedings to both EI and ISTP for indexing.
ICNC'09-FSKD'09 aims to provide a high-level international forum for
scientists and researchers to present the state of the art of
intelligent methods inspired...are encouraged to propose invited sessions. The first author
of each paper in an invited session must not be affiliated with an
organization in China. All papers in the invite…
updated 16.8 years ago • ICNC'09-FSKD'09
<div class="preformatted">Dear List,
I do know that this question has been approached before, but am not
sure about
the reliability of the list of genes.
I have data from an experiment that was run in two batches (3 groups
per batch,
4 samples per group, 2 array-chips per bacth), these need to be
combined and
analysed.
Thus there are 6 groups, and I know from the QC that there is a stron…
VCF requires unique row names, but the formula used to generate placeholder row names can produce duplicates (Such as for pindel with default parameters...code># the forum will likely mangle the TABs in the in-line VCF lines<br/>
test_that("Placeholder names are unique", {<br/>
expect_false(any(duplicated(row.names(.testrecord(c(</code>
<c…
updated 9.7 years ago • Daniel Cameron
Aedin:
I am using the heatplot in made4, and want to output the re-ordered
gene list and column names on heatplot map.
Do you know any commands to do it?
Xiang
</div
peaks.annot)
peaks.annot <- peaks.annot[,-match(c("space", "start",
"end", "width", "names"), colnames(peaks.annot))]
library(org.Hs.eg.db)
peaks.annot$GeneSymbol <-
mget.chain(as.character(peaks.annot$feature...feature",
"Ensembl ID")
peaks.annot <- rename.column(peaks.annot, "peak",
"name")
peak…
updated 13.8 years ago • Mark Cowley
conditions. My first issue is that I would really like the transcript IDs to be replaced by the Gene names. I've used Biomart before to convert the transcript ID to ensmbl gene names in the past. But when I do this, I end up with multiple
updated 3.2 years ago • uhlkatie
Dear user,
I trying to read the intensity by the readillumina package. But there is alway error : "Error in analyseDirectory... Directory does not exist". I am not sure why. I refer to other user have sample problem like me ( https://support.bioconductor.org/p/95307/) but the code of the package was similar with his solution. I am not sure why dose it still happen?
Is it required that the Sent…
updated 4.0 years ago • Đạt
fetch/52447’
retrieving 2 resources
Error: failed to load 'AnnotationHub' resource
name: AH47004
title: clinvar.vcf.gz from dbSNP, GRCh37 assembly
reason: 2 resources failed to download
In addition...messages:
1: In curl::curl_fetch_disk(url, x$path, handle = handle) :
progress callback must return boolean</pre>
With the error message rep…
updated 10.0 years ago • elhananby
cdsBy(txdb, by=„tx).
In the end I want to obtain a GrangesList object with transcript id as names, and start of startcodon and stop of startcodon (+3 nts), which I then can put in the summarizeOverlaps to count features...on strand orientation), and then built a new GRangesList object.
However, as I know R there must be an easier way to proceed. biomaRt from what I saw does …
updated 8.5 years ago • Walter F. Baumann
of chromosome column. Except for the common 22 pairs of chromosome and X, Y, some other chromosome names are strange to me like CHR\_HSCHR17\_2\_CTG5, MT, CHR\_HSCHR8\_3\_CTG1, CHR\_HSCHR7\_3\_CTG4\_4... Could you please
updated 7.5 years ago • xchen8
<div class="preformatted">> Date: Thu, 8 Jun 2006 14:47:09 +0200
> From: Michael Strehle <mstrehle at="" mdc-berlin.de="">
> Subject: [BioC] Subsetting limma TestResults
> To: bioconductor at stat.math.ethz.ch
>
> Dear all,
>
> I recently encountered a problem subsetting limma TestResults on a
> new Bioconductor install. I…
updated 19.5 years ago • Gordon Smyth
<div class="preformatted">Hi Christoph-
Are the aligned read files you are using actually in BED format (chr,
start, end, name, score, strand)?
I'll look into adding an option to allow a .dat extension as an
alternative to .bed; if it is easy (and Gord has time...Hi Christoph-
Are the aligned read files you are using actually in BED format (chr,
start, end, name, score, strand)?
I'll lo…
Hi!
I'm trying to analyse a specific set of CEL files. In these datasets, the effect of a stress agent (H2O2) on yeast performance was tested. There are two control replicates and 4 tests of stress condition done during different time points (15-30-45 and 90 minutes), all with a single replicate. All quality filtering and annotation steps have been done and saved in the file: file_final
I w…
updated 5.4 years ago • June.
following shows that do.call of `c` on a list of IRangesList
returns "list" only when the list is named.
> library(IRanges)
>example(IRangesList)
> class(x)
[1] "CompressedIRangesList"
attr(,"package")
[1] "IRanges"
> class(do.call...c,list(x1=x,x2=x)))
[1] "list"
I am confused this.
I would not expect the fact that the list is named to have any impact
on the result…
updated 13.0 years ago • Malcolm Cook
paste("g", 1:p, sep="") , paste("s", 1:n, sep="")))
\#\# genes in set1 are expressed at higher levels in the last 10 samples
y\[geneSets$set1, (nGrp1+1):n\] <- y\[geneSets$set1, (nGrp1+1):n\] + 2
\#\# build design matrix
design <- cbind(intercept
1.1056984 1.1096023
My question:
Using annotation package how can I convert the probe
ID's to Gene names. how do i incorporate gene name in
place of 100_g_at?
2. How can I choose/filter P-values from T-test that
are less than 0.01
updated 21.3 years ago • James W. MacDonald
Recent ...
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Answered here: https://support.bioconductor.org/p/16318/
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