by
default, or accept an array of filenames. My filenames are the barcode
of the LDA, not the sample name.
In readCtData is there a way to assign sample = from a column within
the
data files?
Regards,
RH
</div
Order by: Relevance
lcpm<-cpm(y, log=T)
head(lcpm)</pre>
gives first row with unique numeric ID which denotes gene names from data file. How to export name of genes into \*.csv file but with name of genes ?
<pre>
write.csv(highly_variable_lcpm, row.names
updated 7.6 years ago • Björn
line-height:1.6">Professor Job Dekker's lab is looking for several bioinformaticians, up to the level of research assistant professor. Experience with deep sequencing, high performance computing and algorithm
updated 10.0 years ago • Julie Zhu
<div class="preformatted">Hi Steffen et al,
Quick question about a search query via biomaRt. Here is the code that
I am
using:
*****
library(biomaRt)
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
filters = listFilters(ensembl)
attributes = listAttributes(ensembl)
getBM(attributes=c("ensembl_peptide_id", "entrezgene",
"ensembl_gene_id", "hgnc_automatic_gene…
updated 15.8 years ago • Tony Chiang
Hi,
I am trying to address the question which genes associate with change of the metabolite levels following the diet. I have paired samples (before and after the diet). I have previously asked about possible adjustments...in my university told me that in lm I should use my dependent variables (like glucose and insulin levels, BMI or said Metabolite) in the "raw" from- meaning untransformed.
…
updated 5.1 years ago • anna.cot.anna.cot
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20080407/
e5a2c438/attachment.pl</div
updated 17.7 years ago • Keyel, Peter
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070625/
b5639236/attachment.pl</div
updated 18.5 years ago • James Anderson
div class="preformatted">Hi BioC,
How can I access gene names from KEEG Gene ID ?
for example : KEGG Gene ID : mmu:11479
Thank you in advance,
Saurin</div
updated 20.8 years ago • SAURIN
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
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Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071026/
7cd3df77/attachment.pl</div
updated 18.1 years ago • Stacey Burrows
SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 4957 features, 999 samples
element names: counts, normalizedCounts, offset
protocolData: none
phenoData: none
featureData: none
experimentData: use 'experimentData...SeqExpressionSet (storageMode: lockedEnvironment)
assayData: 4957 features, 999 samples
element names: counts, normalizedCounts, offset
protocolData: none
…
updated 6.7 years ago • jens
Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData</span>
I don't get error at all, as far as I know, all variables in the design formula (condition here) ARE
updated 9.6 years ago • wannes.nauwynck
What I currently have are all the NM\_\#\#\#\# and NR\_\#\#\#\# for the genes, but I need the gene names. I was able to get a .csv that had quite a few, so I just used R to search (grep) and match the names for me, but the file does not have...I'm hoping there is a function that allows me to input, for example, NM\_001001130, and the gene name Zfp85 would be returned.
Thank you in advance for yo…
updated 10.6 years ago • n_bormann1
all assume
near-constant expression across the design, which is violated by our
(nuisance) block-level differences in composition. We see this when
we
compare edgeR TMM-normalized log(cpm) to qRT-PCR data; the
TMM-normalization
updated 13.1 years ago • Aaron Mackey
vignettes and other questions but I am still confused on what to do
donor(genotype) with 2 levels "WT" and "imKO",
condition with 3 levels "naive" "cisplatin" and "cispAIBP",
My `design = ~donor +condition + donor:condition`
and my...to know the effect of each condition regardless of genotype but most the effect inside each genotype level. will the idea below work?
I understand res_cis…
exptData(0):
assays(1): counts
rownames(25192): A1BG A1BG-AS1 ... ZZEF1 ZZZ3
rowData metadata column names(0):
colnames(103): 169377_LYMPHO_B_accepted_hits.bam
169377_celltype1_accepted_hits.bam ...
999046_celltype_m_accepted_hits.bam...999046_celltype_n_accepted_hits.bam
colData names(2): sizeFactor celltype
> genex<-DESeq(genex)
using pre-existing size factors
estimating dispers…
div class="preformatted">Hi,
is it possible to read a file for the sam calculation with the gene
names in the
same table.
The first column was with gene names, the next four were with
experiments and
the next 14 were the controls...this message:
Fehler in adjust.for.mt(data, cl, var.equal = var.equal) :
The length of cl must be equal to the number of columns of
data.
Zus?tzlich: Warni…
updated 20.1 years ago • Assa Yeroslaviz
and normalization"
[1] "Reading normalization parameters"
list()
Using normalization method: p
[1] "Name the output file"
[1] "hps-d4-mwg-p4-slide26-10"
[1] "Name of output device"
[1] "diagPlot.hps-d4-mwg-p4-slide26-10.png"
[1] "start layout...1] "start 1"
[1] "start 2"
Error in seq.default(0, 1, length = min(17, maxcnt)) :
Length must be non-negative number
In addition: Warning messa…
updated 20.8 years ago • Georg Otto
Could somebody advice me?
Here is the R:
library(SPIA)
x=topTable(fit,coef="WThypo",n=1003)
names(x)
names(x)
[1] "ID" "Gene.title" "Gene.symbol"
[4] "Gene.ID" "UniGene.title" "UniGene.symbol"
[7] "UniGene.ID" "Nucleotide.Title" "GI"
[10...x' in selecting a method for
function 'as.list': Error in .checkKeysAreWellFormed(keys…
updated 14.3 years ago • Jing Huang
dds$Treatment<-relevel(dds$Treatment,ref="Unburned")
levels(dds$Treatment)
dds$TimePoint<-relevel(dds$TimePoint,ref="T1")
levels(dds$TimePoint)
***# calculate geometric means prior...dds, test= "LRT", fitType="local", reduced = ~ Treatment)
resultsNames(dds)
res = results(dds, name="Treatment-Burned_T2")
res1 = res[order(res$padj, na.last=NA), ]
alpha = 0.05
sigtab =…
div class="preformatted">An embedded and charset-unspecified text was scrubbed...
Name: not available
Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070531/
aeb00906/attachment.pl</div
updated 18.5 years ago • Wei Shi
Dear Florian,
I would like to show the common name of genetic elements and not the UCSC's identifier (I think it is what we see).
In addition, I would like to know if it is possible...start, to = end, trackType = "GeneRegionTrack", rstarts = "exonStarts", rends = "exonEnds",
gene = "name", symbol = "name", transcript = "name", strand = "strand", id = "name", name = "UCSC Genes",stacking="pack"…
I can filter these easily).
```r
alTrack <- AlignmentsTrack(alignment.bam, showIndels=TRUE, name="Indels")
plotTracks(alTrack,
from = 1,
to = 12000,
chromosome = "ABC")
```
Thanks already for any advice
unnecessary, just because the @cdfName slot of the
AffyBatch object didn't necessarily match the name of
the R package containing the CDF information.</div
updated 21.5 years ago • James Wettenhall
Done!
[IFNO] Estimating transcription start position...Error: subscript contains invalid names
```
Traceback:
```
Error: subscript contains invalid names
15.
stop(wmsg(...), call. = FALSE)
14.
.subscript_error("subscript contains...subset_along_ROWS(x, i, drop = drop)
7.
cov.frags[chrs]
6.
cov.frags[chrs]
5.
lapply(names(cov.frags[chrs]), function(x) { Views(subject …
updated 6.1 years ago • jason.williams
Reading ... 6Hs.243.1.gpr
> maQualityPlots(mraw)
Error in match.arg(antialias, aa.win) : 'arg' must be of length 1
> maQualityPlots(mraw,DEBUG=TRUE)
[1] "function starting"
[1] 23184 6
[1] "Re-evaluate Weight"
check Control color...and normalization"
[1] "Reading normalization parameters"
list()
Using normalization method: p
[1] "Name the output file"
[1] "6Hs.195.1"
[1] "Nam…
updated 13.3 years ago • Guest User
Hi, I'm using DESeq2 to identify differentially affected histone modifications in cells from control and treated human populations. I have 10 control and 10 treated ChIPseq datasets. I've done the analysis in two ways, the only difference being how the data were initially mapped to the genome.
In the first instance there was no threshold for sequences mapping to mu…
updated 10.9 years ago • David Auble
ht", readfile1 = reads1, readfile2 = reads2, input_format = "FASTQ", :
The number of input file names is different from the number of output file names
<div class="preformatted">Dear all
unfortunately I did not get any reply on my post, so thats why I am
asking
again,
assuming that lots of people already came across that problem.
Working with an array set ( cDNA or any single color platform) just
means
that the probes you are interested in, are spread out over more than
one
array
(usually due to space limitations),
So sample samples, but…
updated 16.2 years ago • Tefina Paloma
Exciting [opportunity for a Computational Biologist at Denali Therapeutics](https://www.denalitherapeutics.com/job?id=2449299) in South San Francisco, CA, USA:
>Do you enjoy analyzing and integrating high-dimensional human data? Then help us identify & validate biomarkers to defeat neurodegeneration!
[Apply online here!](https://boards.greenhouse.io/dnli/jobs/2449299)
### …
updated 5.0 years ago • sandmann.t
x=ss_beads, y=bc_ms)
**Error in vapply(bc_ms, function(x) which(ms == x), numeric(1)) :
values must be length 1,
but FUN(X[[2]]) result is length 2**
I noticed that the ss_beads@parameters@data[["name"]] is a character where as for the...ss_exp@parameters@data[["name"]] it is a factor.
I tried to change it to a factor, but this didn't seem to help.
ss_beads@parameters@data[["name"]]…
updated 6.8 years ago • j.krop
rep(rv[[i]], numNodes(g))
+ } else {
+ if (length(rv[[i]]) != numNodes(g))
+ stop("Attribute vector must have as many elements as 'g' has
nodes.")
+ }
+ names(rv[[i]]) <- nodes(g)
+ nA[[ names(rv)[[i]] ]] <- rv[[i]]
+ }
+ nodeRenderInfo(g) <- nA
+ return(g)
+ }
> toyDrawn <...Rgraphviz_doLayout", graph, as.integer(type), PACKAGE =
"Rgraphviz")
2: graphLayout(g)
…
br/>
Error in getPromoters(organism) : <br/>
The input parameter needs to be a valid genome name ('dm3', 'mm9' or 'hg19') or a set of background sequences.</code>
My question is what structure is "a set of background
0 0 0 0
<strong><span style="background-color:Yellow">> clr.tbl<- validate(mycounts,mycounts1)
Error in validate(mycounts, mycounts1) :
argument 'tnet' must contain values 0 or 1</span></strong>
</pre
updated 9.9 years ago • Angel
are not annotated with gene model), I thought about comparison read counts at the single nucleotide level (therefore comparison of sequencing depth) and applying some thresholds (p-value or test statistics) to define differential
Hi All
I have performed gometh on a 450k methylation dataset and extracted the top 20 categories using topGO. My question is, is there a way to generate a list of the gene names in the returned "DE" column, for examples the 71 genes reported in the below example?
Term  ...the top 20 categories using topGO. My question is, …
updated 8.7 years ago • r.clifford
quantity, betaPrior = TRUE, maxit = 1000) </pre>
I'm interested in changes in expression between levels of the `` stage `` factor. I can extract results for Primary Branch Meristem vs Secondary Branch Meristem and Secondary...contrast = list('stagePrimary.Branch.Meristem', 'Intercept'), alpha = 0.05) `` or `` results(dds, name = "stagePrimary.Branch.Meristem", alpha = 0.05) ``?
Thanks for…
updated 10.9 years ago • Tom
The codes and instructions for annotating gene names to the result table for differential gene expression analysis in DESeq2 seem to be for using Ensembl as the reference...genome in the alignment step. I'm wondering if there are instructions/codes for annotating gene names if I used UCSC hg19 as the reference genome in the alignment step? Thanks for your help
updated 10.7 years ago • anpham
Hi good evening,
I want to replace special characters in row names (.30.) by (-30-)
for example:
`tag.30.gvs`
by
`tag-30-gvs `
for large data frame have more that 300 rownames all needs replacement...Hi good evening,
I want to replace special characters in row names (.30.) by (-30-)
for example:
`tag.30.gvs`
by
`tag-30-gvs `
for large data frame have more tha…
updated 5.8 years ago • ph.shimaasherif
but it failed because of the
following error.
Error in array(x, c(length(x), 1L), if (!is.null(names(x)))
list(names(x), :
attempt to set an attribute on NULL
Calls: topTable ... toptable -> as.matrix -> as.matrix.default ->
array...lt;- avereps(normdata, ID=normdata$genes$ProbeName)
condition <- factor(targets$Condition, levels =
unique(targets$Condition))
design…
_pseudotime\_ are compared, right? Even so, how do I know which of the two branches are assigned the names of 'Cell fate 1' and 'Cell fate 2' (apart from manually running </span>buildBranchCellDataSet and checking out which of the...branch_labels = c("Activated", "Latent")
+ )
Error in as.igraph.vs(graph, from) : Invalid vertex names</pre>
I genuinely cannot understand the document…
updated 8.4 years ago • kevin.rue
Secondly, when i use the reportHTML on my mQC file, the following error appears
> Error in names(miss.df) <- c("x", "y") :
'names' attribute [2] must be the same length as the vector [1]
Looking into the names, there is an obvious difference
updated 6.1 years ago • laural710
<div class="preformatted">Hi,
I am interested in annotating lists of SNPs in R, mostly I am
interested in finding the gene a SNP is located in and for intergenic
SNPs which genes are close by. I found this code that wsa developed
with the help of Valerie Obenchain:
http://adairama.wordpress.com/2013/02/15/functionally-annotate-snps-
and-indels-in-bioconductor/
However, when I adapted this…
TxDb.Hsapiens.UCSC.hg19.knownGene, by = "gene")
unlist(exons)
# this will lost the gene name information.</pre>
How do I add the name of the gene for the exons?
I have read https://www.biostars.org/p/101513/ and 
updated 8.1 years ago • tangming2005
DataFrame` via `unsplit()`.
`unlist()` will coerce back to `DataFrame` but flips the row names, because we're not keeping track of our factor grouping:
```r
unlist(split, use.names = FALSE)
```
```
DataFrame with 4 rows and 2 columns...df[["b"]])
```
```
## Error in unsplit(split, f = df[["b"]]) :
## Length of 'unlist(value)' must equal length of 'f'
```
```r
unsplit(spl…
preformatted">
I was wondering if there is some way of getting the XPS package
working at gene level as I need to get the gene expression from some
Rat Gene chips (RaGene 1.0 ST r4)that I will analyze.
I tried to use the Affy
div class="preformatted">Hi,
I am trying to get the gene symbols and names of genes included in the
TopTable. I am using affylmGUI package under R 2.9.1 on windows XP.
Even
after downloading the
updated 16.3 years ago • Kai Treuner
2 or 3 replicates- so
my read of literature is p values not very useful here).
Seems to me there must be a more statistically valid approach or one
which somehow weighs degrees of correlation across all comparisons and
numsamples ) )
newMf$dispersion <- dispsThis\[match(newMf$exon, names(dispsThis))\]
newMf$count <- as.vector( countsThis )
newMf <- droplevels(newMf)
 ...the new object have its sample column (factor) reordered in an alphabeti…
updated 9.9 years ago • gmerino
On 08/07/2015 11:14 AM, tom carroll wrote:
You can provide your own annotation in the form of a named list of GRanges with the first element of the list containing a character vector of version.
I include an example below...You can also provide your own denovo List of GRanges but first
element must be a character with name "version".
library(GenomicRanges)
library(ChIPQC)
customAnnotati…
affy.object,file=paste(experiment.designator,
"AffyQCReport.pdf", sep="."))
Error in attr(groups, "names") <- names : 'names' attribute [29] must
be
the same length as the vector [1]
Enter a frame number, or 0 to exit
1: QCReport(object = affy.object...paste(experiment.designator,
"AffyQCReport.pdf", sep = "."))
2: signalDist(object)
3: boxplot(object, names = ArrayIndex, ylab = "Log2(In…
Affymatrix ids, I found out that there are multiple affymetrix IDs corresponding to a single gene name for a sample. My work revolves around gene names only. Please suggest the appropriate step to deal with this situation
updated 20 months ago • Reeya
library). I isolated RNA from the same type of tissue across different individuals. There are three levels for one condition ("behavior"), and 4-6 biological replicates per level. I assessed the quality of the data using DESeq2
BioMart database will fix it's current Ensembl 47
release with the following attribute/filter name changes involving
gene
symbols.
* For the hsapiens_gene_ensembl (human) dataset you'll need
hgnc_symbol
as attribute...and filter name to use/retrieve gene symbols.
* For the mmusculus_ensembl_gene (mouse) dataset you'll need the
mgi_symbol as attribute...and filter name (this was markersymbol in
p…
than "gMDSC from ascites".
Here's a (not complete) exemple of my annotation df, with sample names as rownames.
cell_type cond origin group
CA.gMDSC.Blood gMDSC Cancer_Blood 1 gMDSC_Cancer_Blood
DE.gMDSC.Ascites...A03.gMDSC gMDSC Ascites 2 gMDSC_Ascites
With…
updated 5.7 years ago • christophe.vanhaver
r
for (cond in 1:length(pair_names)){
CONTRASTS = makeContrasts(pair_names[cond], levels = design )
contrast= CONTRASTS[CONTRASTS[,1] != 0,]
names(contrast)
contrast_pair = c(names(contrast))
res_edgeR = exactTest(edgeR_obj
updated 2.7 years ago • f_rahmdani
span style="line-height:1.6">Dear all,</span>
I am trying to load a database, which name is in a variable (I actually ask the user to provide the name of the database he needs). Does any body know if this is even possible
updated 11.0 years ago • Patrick Schorderet
expression ("Profile") whilst covarying for the effect of institution where sequencing happened (3 levels), gender (2 levels), age bins (5 levels), RIN (continuous), post-mortem interval (PMI, continuous), and five population covariates...Institution <- factor(pd_nodups$Institution)
pd_nodups$Profile <- factor(pd_nodups$Profile, levels = c("Control","Condition"))
pd_nodups$Gender …
updated 7.0 years ago • rodrigo.duarte88
Now that I made sure there are enough sites to allocate all the samples it tells me that the layout must match exactly with the number of samples to distribute on the plates..
``` r
library("Omixer")
data(survey, package = "MASS")
survey...Error: Problem with `filter()` input `..1`.
#> ℹ Input `..1` is `mask == 0`.
#> x Input `..1` must be of size 288 or 1, not size 237.
Omixer_ind…
updated 4.4 years ago • Lluís Revilla Sancho
samplePattern = "PSC", pData = pheno\_data) :
first column of pData does not match the names of the folders containing the ballgown data.
In addition: Warning message:
In ballgown(dataDir = ("C:/ballgown"), samplePattern...to look at my loaded \_phenodata.csv in R, I see 1st column is 1-38, my samples. 2nd column is the name of the sample dir from my stringtie -e -B …
updated 7.4 years ago • harris
<div class="preformatted">
The first problem I have was with ideoTrack. I am using
genome<-'danRer7' and when I perform:
> genome<-"danRer7"
> myGene<-getGenes(cuff_data,'cdk6')
> myChr<-unique(features(myGene)$seqnames)
> ideoTrack <- IdeogramTrack(genome = genome, chromosome = myChr)
I receive the following error message:
Er…
Recent ...
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