div class="preformatted">Hello,
I have used the 'names' function in flowViz to place percents of the
gated population within the plot. I have never figured out how to get
the...plot automatically, but at least I could place
the numbers in the plot. With quadrantGate plots the 'names' function
does not appear to do anything. Is there a mechanism to access this
and
label the plot quadrants?
Th…
Order by: Relevance
GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1178100 features, 90 samples
element names: exprs
protocolData
rowNames: 75_459_CD16.CEL 76_460_CD16.CEL ...
triad0078_H7_498_CD16.CEL (90 total)
varLabels...GeneFeatureSet (storageMode: lockedEnvironment)
assayData: 1102500 features, 33 samples
element names: exprs
protocolData
rowNames: TisMap_Brain_01_v1_WTGene1.CEL
TisMap_Brain_02_v1_…
div class="preformatted">
I have been using beadarray v. 1.5.10 to analyse bead-level Illumina
data.
At the moment the package does not support bead-level normalisation
for
single channel data. As I would...be very interested in getting data
quantile-normalised
at the bead-level, before summarising, I would like to know if there
are plans in the near
future to add this feature in to the packag…
_Error in new\_Hits(Class, from, to, nLnode, nRnode, mcols) :
'nLnode' and 'nRnode' must be single integers)_ which I am not sure how to resolve.
__distanceToNearest(myRanges1, myRanges2, ignore.strand...Error in new\_Hits(Class, from, to, nLnode, nRnode, mcols) :
'nLnode' and 'nRnode' must be single integers__
__myRanges1__
…
updated 9.2 years ago • roladali
nbsp;
> BiomartGeneRegionTrack(genome=assembly,biomart=mart,chromosome=chrom,start=start,end=end,name="ENSEMBL genes")
Error in getBM(attributes, filters = filterNames, values = filterValues, :
Invalid...attribute(s): external\_gene\_name
Please use the function 'listAttributes' to get valid attribute names
> traceback(…
Hello,
I have multi level experiment limma design. I want to ask after I create fit object by `` fit <- lmFit(v,design,block=targets$Subject,correlation
updated 9.4 years ago • zzjerryzhang
account the samples that are from the same patient.
First, I have followed the section 9.7 multi-level experiments from the limmat manual in order to do pairwise comparisons:
```r
Treat <- factor(paste(targets$Time,targets...Time1.Highdose-Time3.Highdose,
Time2vsTime3forhigh= Time2.Highdose-Time3.Highdose,
levels=design)
fit2 <- contrasts.fit(fit, cm)
fit2 <…
updated 4.7 years ago • ellen2270
rowNames: EC01_Batch02.fcs EC02_Batch02.fcs ... YC23_Batch11.fcs (91 total)
varLabels: name
varMetadata: labelDescription
column names:
Time, Event_length, Y89Di, Pd102Di, Pd104Di, Pd105Di, Pd106Di, Pd108Di, Pd110Di...Offset, Width, Residual
```
My batch.comp is a list of factors, where one factor contain the names of all files from the same batch, and one factor is used to re…
updated 6.6 years ago • Florent
Hi.
How to convert 'lncRNA probe name (ex. p2966)' or 'mRNA probename (ex. A_19_P00315593)' to gene symbol?
I use 'GSE115018' data for practice.
To convert probe name to...biomaRt', 'org.Hs.eg.db' and etc. package.
Which package should I use to convert probe name into gene symbol
updated 2.8 years ago • Sooni
specific question but I would like to
seek
suggestions about the pipeline to analyze transcript level DE
analysis.
I generally use Bowtie -> Rsubread -> edgeR pipeline for gene level
DE
analysis.
Could someone please suggest...the steps/pipeline for Transcript level
differential expression analysis?
Thank you,
Alan
[[alternative HTML version deleted]]
</div
to use DESeq2 to process three bulk RNASeq paired samples but I am trying to figure out what is the valid model to use here. I used tximport to import Kallisto's transcript-level abundance estimates at gene level to use with
updated 6.4 years ago • Puks
<div class="preformatted">Hi,
I am a very stupid beginner trying to get started and I am trying to
figure
out how to do probe level normalisations like RMA with Nimblegen
arrays. Is
there anybody out there with experience in Nimblegen arrays to give...Hi,
I am a very stupid beginner trying to get started and I am trying to
figure
out how to do probe level normalisations like RMA with Nimb…
Hi,
is it possible to compare this 7 factors (levels) at once?
dds$brain_areal = factor(dds$brain_areal, levels = c(**"primary and secondary corticies","limbic and association
updated 2.3 years ago • melander
answer so I posted here
and hope
to get some suggestion..
I intend to extract GO terms at different level of GO's DAG; for
example, I
would like to know within BP, at the level of 3 to 5, what those GO
terms
are and what entrezgene ids
in transformRNAseq(y = y, normFactors = normFactors, transformation = "profile", :
‘normFactors’ must be one of
the following: none, TC, DESeq, TMM, or a vector oflength equal to the number of columns
in ‘y’
```
Looking at the code, I did...specify a valid option for normFactors, but R is registering as invalid.
Users of coseq, any thoughts as to why this problem might be …
makeTxDbFromGRanges(test)
Error in .get_cds_IDX(type, phase) :
the "phase" metadata column must contain 0, 1, or 2, for all the CDS features</pre>
However, when I check the GRanges object, everything seems to be in order:
<pre
updated 7.3 years ago • bbrink
Xiayu
Sent: Monday, July 28, 2014 4:55 PM
To: bioconductor at r-project.org
Subject: [BioC] multi-level design and contrasts problem - limma
Hello,
I read the limma user guide on the topics of multi-level experiments
and found...and set contrasts
normal-tumorPos for (2) and normal-tumorNeg for (3). Or I should
follow the multi-level design instructions to include the type_AR and
chip in the des…
updated 11.4 years ago • Rao,Xiayu
type.
I constructed the contrast matrices (see below in the code and
results) without knowing their validity.
Are they right?
Part of my code and results are as follows:
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-pc-mingw32...WU MU 7.gpr
8 MU WU 8.gpr
> design<-modelMatrix(targets,ref="WU")
Found unique target names:
MS MU WS WU
> design
MS MU W…
type.
I constructed the contrast matrices (see below in the code and
results) without knowing their validity.
Are they right?
Part of my code and results are as follows:
> sessionInfo()
R version 2.6.2 (2008-02-08)
i386-pc-mingw32...WU MU 7.gpr
8 MU WU 8.gpr
> design<-modelMatrix(targets,ref="WU")
Found unique target names:
MS MU WS WU
> design
MS MU W…
everything works smoothly. However, the resulting exprs object contains data on the probeset/exon level (analogous to the Gene Expression Omnibus annotation file GPL17585), rather than on the gene/transcript level (as in GPL17586...How could I use SCAN.UPC to generate transcript-level data? The number of probesets (925032) in the data returned by SCAN is huge, and I would prefer the transcript-le…
updated 7.9 years ago • Lukas__
cryptic error messages. After tracking down the problem I found out that this was due to the file names I used.
My file names started with numbers and contained "-" signs. In the r3Cseq pipeline the filenames are used to name the...matrices and files that are created. By default R changed the file names by adding X in front of the numbers and replacing "-" by ".". As a result the r3Cseq package …
updated 10.6 years ago • felix.klein
Computational Biology. The appointment will be made at the ASSISTANT,
ASSOCIATE
or FULL PROFESSOR level. The successful candidate will join an
innovative and
multidisciplinary Institute for Integrative Genome Biology...program, have a strong commitment to excellence in teaching
at the undergraduate and
graduate levels, and participate in departmental and interdepartmental
graduate programs.
Appli…
updated 18.1 years ago • Thomas Girke
div class="preformatted">Dear Bioconductor,
I usually obtain exon-level/gene-level signal using Plier/RMA
implemented in Affymetrix's Expression Console, however there is no
way to get probe...level intensity from it. Does anybody know how to get
probe level intensity from Affymetrix Exon Array platform?
Thanks,
Shirley
attribute: affy_zebrafish not found, please use the function
'listAttributes' to get valid attribute names
Then I use listAttributes() as requested:
>listAttributes(mart=mart)
and get the following output:
<snip...attribute: hgnc_symbol not found, please use the function
'listAttributes' to get valid attribute names
Any hint will be appreciated.
Best,
Georg
> sessionInfo(…
Hello,
I am using edgeR to calculate differential gene expression among individuals from two populations (BR and SD) exposed to three salinity treatments (15, 35, 60 ppt), with three biological replicates each (a, b, c) for 18 samples total. When I create my design matrix, my six treatments are named with numbers, but in the edgeR documentation, the treatments are named with letters, fo…
Dear community,
is it possible to use RMA to get exon-level summaries for the HTA 2.0 platform in Bioconductor?
I would like to run diffSplice() from limma to detect genes that have...differential splicing between two conditions and I need an expression matrix with counts at the exon level for that.
I have already used RMA on the probeset/transcript cluster level using the Affymetrix hta20…
updated 8.2 years ago • relathman
div class="preformatted">HI,
Does anybody know how to control the order of the column names
displaying in the heatmap (heatplot)?
I was trying to compare two heatmaps with same set of genes as row
names and same set...of patient samples as column names. The result
shows a different order of column names.
I want they display in the same order in the heatmap pictures.
regards
updated 15.3 years ago • xiangxue Guo
and recommended workflow using the `catchSalmon` and `catchKallisto` functions for differential tx-level analysis with `edgeR`. The manual mentions but does not offer any details on the functions.
`help()` mentions that a per-transcript
updated 5.1 years ago • ATpoint
div class="preformatted">I don't know of any packages designed for probe-level analysis, nor do
I
know what you mean by SFP detection.
However, if you just want to use the probe values for analysis you...All,
>
> I am using Affy GeneChip for SFP detection and only interested in
the
> probe-level data. Who knows there are some PCA packages or tools
that
> can analyz…
<div class="preformatted">Hello all,
I do need some help on analyzing such unorganized data. Please help me
out. Thank you so much!
I basically followed the analysis of multi-level experiments in limma
user guide. But I do not feel right about the code below. Please give
me some suggestions.
# I want to compare Normal vs. Tumor negative, and Normal vs Tumor
positive. There are partial pa…
updated 11.4 years ago • Rao,Xiayu
gt; txdb= makeTxDbFromUCSC(genome= "hg19", tablename="ensGene")
Error in names(trackIds) <- sub("^ ", "", sapply(nodes, xmlValue)) :
'names' attribute \[211\] must be the same length as the vector \[209\]
any ideas how
updated 8.0 years ago • arko.sen1
So I have around 70000 probesets, but then, how can I calculate the expression indices at transcript level? Is there any function? As far as I know, featureFilter returns the probeset with the greatest variance, for a given transcript
updated 10.1 years ago • jacorvar
ENSG00000000005 ... ENSG00000273492
ENSG00000273493
rowData names(9): gene hgncl ...
colnames(100): 1 1 ...
99 100
colData names(13): ID SAMPLE
I have tried:
data_matrix <- data@assays[[1]]
data_filtered...data_matrix))>1,]
but got an error:
Error in count(data_matrix) :
Argument 'x' must be a vector…
updated 6.1 years ago • annkolman78
div class="preformatted">Dear all,
I have the following probe names selected from a dataset (GDS592),
taken from GEO (SOFT format).
gnf1m29878_a_at
gnf1m13556_at
gnf1m09610_a_at
gnf1m11352_a_at...gnf1m26036_at
...more...
And I want to get the GO term and Official Gene Name from these
probe names.
Is there a way to do it?
I tried these two Bioconductor commands but fail.
> library(…
I'm trying to create an `` hdf5 `` file using `` R ``'s `` rhdf5 `` package.
I want to create this `` group `` hierarchy: `` "top/bottom" ``. In `` "bottom" ``, I'd like to have two datasets (both `` H5S_SCALAR ``s):
1. `` "score" `` which is an `` "H5T_IEEE_F64LE" `` type
2. …
updated 7.6 years ago • rubi
dataset is Ensembl_ID. You could use getBM function in
biomaRt
package to convert ensembl_ID to gene name or other IDs if needed.
Best regards,
Julie
On 1/19/11 2:10 PM, "Pablo Echeverria" <pablo.echeverria at="" unige.ch="">
wrote:
> Dear...that are described in your paper (those are
already
> working), but also I need to retrieve gene names associated to my
peaks.
&g…
updated 14.9 years ago • Julie Zhu
timepoint 2, which I got from the interaction term Treatment:Time
```r
resT1 <- results(dds, name="TreatmentInfected.Time1", test = "Wald")
resT2 <- results(dds, name="TreatmentInfected.Time2", test="Wald")
```
It was a bit unclear
updated 12 months ago • Jason
div class="preformatted">Dear all,
I can not change the list element names of my GAlignmentsList objects:
library(GenomicRanges)
library(Rsamtools)
ex1_file <- system.file("extdata", "ex1.bam...Rsamtools")
ga <- readGappedAlignments(ex1_file)
galist <- GAlignmentsList(one=gal, two=gal)
names(galist)
names(galist) <- c("three", "four")
Error in `names<-`(`*…
updated 12.1 years ago • Hans-Ulrich Klein
10.1101/2020.10.30.362533v1.full
Unfortunately, we recently didn't check for conflicting package names on CRAN and meanwhile a package with a similar name was accepted:
https://cran.r-project.org/src/contrib/Archive/rawr...ERROR
Maintainer: 'Christian Panse
<cp@fgcz.ethz.ch>'
New submission
Conflicting package names (submitted: rawR, existing: rawr [https://CRAN.R-project.org])
…
updated 5.0 years ago • Tobias
are not 'stand alone'. Although Affy intends ADS
and
SI to be their quantitative measures of mRNA level, these measures go
hand
and glove with thier respective absence calls. As far as what the
absence
calls mean, there appears...gt;From: "Crispin Miller" <cmiller@picr.man.ac.uk>
>Subject: [BioC] replicates and low expression levels
>To: <bioconductor@stat.math.ethz.ch>
…
<div class="preformatted">Hi All
I have cufflinks generated transcripts file in gtf format. I wondering
if I can use any R package to convert it to gene level gtf file. By
this means all the transcripts are collapsed into genes and each gene
contains all the exons seen in all the...transcripts file in gtf format. I wondering
if I can use any R package to convert it to gene level gtf file. …
packages/release/data/annotation/
Almost Genome wide annotation packages following the name convention
org.species.eg.db. I'm wondering why org.At.tair.db is named
differently. Should its name be modified to
updated 13.4 years ago • Peng Yu
Invalid attribute(s): CHO_symbol
Please use the function 'listAttributes' to get valid attribute names
I know the common symbols such as mgi for mouse, rgd for rat and so on, not sure what it is for the chinese
div class="preformatted">hi members,
i am looking for a function which plots me average probeset levels
with
standard deviations (e.g. tissues 1 against tissue 2). Is there any
functions which could do this. i work with affymetrix...now i would like to have the average values with the standard
deviation
for these probeset_id log levels to plot e.g. two tissues (here heart
and breast) against …
updated 17.8 years ago • Paul Hammer
correctly, KEGG has a hierarchy/classification for the pathways. For example. In the first level we have Metabolism, inside this category, in the second level we have Carbohydrate metabolism and in the third level...get_htext?br08901)
I was wondering if there is a way to tell kegga that we want an specific level for the results.
Thank you.  
that align to the features (exons) of a meta-feature (gene).
However my output file is at the exon level (sorry for the line formatting in the screenshot):
![featurecounts Output][1]
I can't tell if this is an issue with featurecounts
updated 2.6 years ago • CDSPARKS
affy to analyze some arrays, and I want to do mva plots.
I am trying to change the hybridizations names in the first row of the
exprSet, as I dont want to plot the PATH to my CEL files, but just a
legend.
I have tried to change these...names by accessing the elements of the
first row in the exprset, but I dont get them.
>exprs(L3hRMA)[0,]
/home/Genechip/LA_03h_02.CEL
Hi,
I got `` Length of 'group' must equal number of columns in 'counts' `` with the below code.
> targets <- read.delim("phenoSp.txt", stringsAsFactors=FALSE...lt;- rbind(data, tot.counts=colSums(data))
>
> # inspect and look at the top row names!
> print("!!! data <- rbind(data, tot.counts=colSums(data))")
[1] "!!! data &…
updated 8.3 years ago • mictadlo
in the design formula. Essentially I want to use deseq2 to set up contrasts among the treatment level . Is the following code valid ?
```r
If a design formula is specified, it must be composed from the following allowable factors
in the chemistry/instrumentation is enough to be a
rather large component of variance) and has three levels. By three
levels, I mean there are 2 different treatments and 1 control. When I
push the workflow through, everything works...fine, but I'm having a
hard
time delineating which level is responsible for a gene being
identified
as significantly differentially expressed. I understand that (i…
updated 13.6 years ago • Ingrid Lindquist
genes. However, after the loading the sequences and gff file, the check input command returned " Names of list elements in 'seq' and 'annotation' must match". i have specified the path to both gff and fasta files using
gff_dir...using
check_input(aastringsetlist, grangeslist)
Error in check_list_names(seq, annotation) :
Names of list elements in 'seq' and 'annotation' must match.
…
updated 23 months ago • Sujeevan
div class="preformatted">Hi,
I am using the CMA package to perform internal, Monte Carlo
cross-validation (MCCV) on SVM classifiers in a microarray dataset.
The dataset has numerical, non-NA values for ~400 genes for 45 samples...and I am trying different values for the
training-set fraction. CMA also performs inner-loop validations
(3-fold cross-validation within the training sets, by defaul…
updated 14.8 years ago • Santosh Patnaik
I wanted to ask if the summarisetogene() function would result in sum of transcript level expressions for a gene if both were normalised using the median ratio's method. I know that TPM values follow this pattern...but I wanted to know about this as the sum of transcript level expression differed slightly from the gene level expression.
Thank you for your help
Hi,
I have isoform-level deep RNA-seq data from stringtie on about 800 people. I have created gene-level and isoform-level data using tximport...I have just looked at the voom mean-variance trend plots. At the gene level, the plot looks as usual (decreases at low expression levels and then levels off). For the isoform data, the plot looks different...the fit curve continues to decrease all along…
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.
```
Here is the code I'm using:
```
genes <- select...I've tried several different dbs but none of the could give me gene symbols.
Here is the row names (geneIDs) which I honestly do not even know what keytype …
status = factor(c(rep("case", ncol(case_frame)), rep("control", ncol(control_frame))), levels = c("control", "case"))
)
# Merge the case and control frames
data <- rowmerge(case_frame, control_frame, all = FALSE) # inner merge...the order of the cols and rows is the same
data <- data[, row.names(metadata)]
# The data must be un-logged
data <- round((2 **…
updated 2.1 years ago • Luca
is
already a contrast vs 1. So
you need
cont.matrix <- makeContrasts(-2,2-3,3-4,4-5,5-6,6,levels=design)
HOWEVER, to make this work the column names of the your design matrix
must start with a letter,
not a number. E.g
is useful, it returns the number of raw reads that align to
each
intron grouped at the transcript level. Is there an easy way to get it
to
group it by a gene such that I am grabbing all the introns that fall
in all
the transcripts...intronic
space).
Similar, is there a way to easily get the raw read count at an
individual
intron level rather than having it grouped? The introns() function
seems t…
updated 12.8 years ago • Fong Chun Chan
probes which individuals, for
example Medicago:AFFX-CreX-5_at:587:698, have high fluorescence
levels and which do not. I realise binding efficiencies differ for
individual probes, but I am only looking for indicative
Hello ...
I have the following chromosome names in my hg19 reference sequence.
<pre>
> names(seqlengths(tx_by_gene))
[1] "chr1" "chr2" "chr3" "chr4" "chr5" "chr6" "chr7" "chr8"
[9] "chr9" "chr10...Hello ...
I have the foll…
updated 11.2 years ago • marcovth
Recent ...
Replies
Comment: How can I correctly use phyloseq with Docker?
by
Suzy
•
0
The graphics in [Snow Rider][1] are colorful and charming, adding to the festive atmosphere.
[1]: https://snowriderio.io
Comment: GOseq Probability Weight Function bad fit
by
ejasge.r.m
•
0
When performing GO analysis with GOseq, i s important to carefully check your input and assumptions, just like reviewing choices on the McD…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study
by
ATpoint
★
5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR
by
efoss
▴
10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Awards
• All
Commentator to
sina.nassiri
▴
130
Popular Question to
Hervé Pagès
16k
Popular Question to
jared.andrews07
▴
30
Popular Question to
shepherl
4.2k
Locations
• All
France, 17 minutes ago
United States, 21 minutes ago
The city by the bay, 25 minutes ago
United States, 48 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
France, 17 minutes ago
United States, 21 minutes ago
The city by the bay, 25 minutes ago
United States, 48 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Traffic: 512 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6