Is this simply because most of the lncRNAs included in the FASTA files are not annotated with gene names? Should I summarize to the transcript level with `txOut = TRUE
Order by: Relevance
dds <- DESeq(pre_dds)
At 24h, I want to get the effect of albumin on Plastic (the reference level), interaction term, and effect of albumin on Host.
The first two work:
results(dds, contrast = c("Group","24h.withAlbumin", "24h.noAlbumin...results(dds, name="MediaHost.Group24h_withAlbumin")
But the last one throws an error:
results(dds, list( c("Group_24h.withAlbumin_vs_24h.noA…
updated 3.3 years ago • gtechbio
The lumi package supports both GenomeStudio and BeadStudio output
files.
We recommend using probe level data, which usually is named as "Sample
Probe
Profile Sample.txt". There are detailed example in the lumi vignette
"Using
new single cell genome and transcriptome methods for tracking clonal trajectories at single cell level in patients and patient-derived xenografts. The post holder will have the opportunity to interact as part of the international...Please put “Single Cell Genomics, Molecular Biology – Aparicio Lab – PDF Position” and your family name in the subject line
updated 6.4 years ago • jmaanaki
DiffTempC = (StimulusC.TempHigh - NegControl.TempHigh) - (StimulusC.TempLow - NegControl.TempLow)
levels = design
)
#Then compute these contrasts and moderated t-tests
fit2 <- contrasts.fit(vfit, my.contrasts)
efit <- eBayes
updated 8 months ago • Elizabeth
the Error is when i want to load bed file with using "readTranscriptFeatures" in Genomation R package
feats = readTranscriptFeatures("gff_assembly_to_bed.bed")
Reading the table...
Calculating intron coordinates...
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
In range 1: 'end' must be >= 'start' - 1.
i checked the bed file there is not values for…
updated 2.9 years ago • sat
1)
Error in DesignPrimers(tiles, identifier = "Accumulibacter", minCoverage = 1, : OligoArrayAux must be properly installed
Dear Everyone,
Could someone please point me to the function within Bioconductor that
allows me to see the individual expression values for each of the
probes on a chip? I have a specific probe I want to look at and I
would like to see the 12-20 perfect match and mismatch pairs for that
probe id.
Thanks,
Richard Park
Computational Data Analyzer
Joslin Diabetes Center
How to perform the normalization using the individual probe expression
values instead of the probeset expression values in Limma or any other
bioconductor package??
Thanks in advance..
Regards,
Suresh
[[alternative HTML version deleted]]
Hi list,
I found the XY coordinates for the probes in 'hgu133aprobe' are not
exactly the same as those shown on NetAffx.com. Please see below.
Also, is the order of the probes from pm(myAffyData, '1007_s_at'), for
examples, the same as in 'hgu133aprobe'?
thanks,
...Tao
> R.Version()
$platform
[1] "i386-pc-mingw32"
$arch
[1] "i386"
$os
[1] "mingw32"
$system
[1] "i386, mingw32"
$status…
lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, :
'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
> raw.data <- ReadAffy()
> eset <<- rma(raw.data)
Error in library("rcapex1a520469fcdf...lib.loc = NULL, character.only
= TRUE) :
'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
>l…
genes (i have chosen the ratio > 2 to be significant in that
particular comparison).
This was a validation assay of our genome wide screen using agilent
arrays. With custom GGMA consisting of 384 probes, we were able to...validate quiet some data and is encouraging, but i have questions
regarding the analysis of ggma data, whether im doing something
updated 16.3 years ago • r.kandimalla
For pathway '05166', the following error message is produced:
<pre>
None of the keys entered are valid keys for 'PATH'. Please use the keys method to see a listing of valid arguments.
</pre>
How to explain that the 'kegga' function
of the "names" are Entrez Gene IDs) that are in category
GO:0006836, and 4 of entries I have marked as significant by setting
their values...lt;- list()
test.stat.BP[1] <- list(new("classicCount", testStatistic =
GOFisherTest, name = "Fisher test"))
result.BP[1] <- list(getSigGroups(BP.GOdata,
test.stat.BP[[1]]))
test.stat.BP[2] <- list(new("elimCount", test…
in the UniProt database.
To be specific; among others I would like to retrieve the preferred gene name, which is labeled "Gene names (primary)" in the resulting table when using UniProt's web-based ID mapping interface.
As example...29%2Cyourlist%28M2015022613L2TBUNHS%29)
As can be seen, this ID links to multiple (13) gene names/synonyms (7th column), but the primary gene name is Psmb9 (5th co…
updated 10.8 years ago • Guido Hooiveld
up to date**? I've tried to make my own genome/object for use with goseq. I have a vector of gene names and lengths, but I cannot figure out how to incorporate GO Terms and then make a suitable 'object' that can be fed into `goseq...1300 fewer genes than my list from sacCer3 (see code).
I assume that my provided gene list must have a matching name within `org.Sc.sgd.db` in order for associate…
updated 4.9 years ago • vanbelj
and par(mai=c(2,0.82,0.82,6)) still no luck.
Don't know how to go about getting the full Gene names displayed on the
tree.
Thanks in advance,
Alan
sessionInfo()
R version 3.2.2 Patched (2015-08-16 r69094)
Platform: x86\_64
updated 10.2 years ago • Alan Smith
nbsp;
I apologise for all the questions, but I have two more!
1) Is there a way to get gene names on the "peaklist" object obtained from the findOverlapOfPeaks function? I'm able to get the peaklist but it's just a very
updated 9.0 years ago • jmKeith
rownames(colData)<-colData$Sample.ID
#checking tha tall rownames in ColData match the column names in genes10
all(colnames(genes10) == rownames(colData))
#omit any NA values
genes10 <- na.omit(genes10)
#condition1 = added...X7.Session>0,1,0))
#dds needs the design to be as a factor. and associates the 0 and 1 levels with learner and non learner
colData$conditi…
updated 2.1 years ago • RHEA
using the MPS files. By calling
core/full/extended in oligo, you're summarizing to the transcript
level, and you should do the same with APT to get comparable results.
Best, b
Sent from a mobile device. Please apologise for brevity...file
with Oligo package and the normalized file with APT, there is a big
difference:
- At CORE level:
* APT: 287 329 probesets
* Oligo package: 22 011 probese…
Dear all,
I want to use cPlot and cColor from the geneplotter package to
visualise the intensity level of some genes from a microarray
experiment on their given chromosomal location. However, I'm slightly
confused by the...as.list(x[mapped_genes])
chr <- buildChromLocation("org.Mm.eg.db")
cPlot(chr)
cColor(probes=names(xx[1:4]), color=c("red", "green", "blue",
"purple"), plotChroms=ch…
updated 17.5 years ago • Heidi Dvinge
my design matrix without an intercept :
> design <- model.matrix(~0+Group) \#Then change the names to remove the "Group" part of the name
And so, I'm interested in the genotype by treatment interaction. What is the correct...mut1\_a"=(mut1B-mut1A)-(wtA-wtB),
"mut1\_b"=(mut1B-mut1A)-(wtB-wtA),
"mut1\_c"=(mut1B-wtA),
levels=design)
Then the fit, etc:
> …
updated 8.7 years ago • joelrome88
<div class="preformatted">Dear Bioconductor:
We have a affymetrix time course experiment with repeated measurements
taken at 0 minutes, 30 minutes and 240 minutes following infusion of
insulin. There are 10 arrays for each time point. We used gcrma to
pre-process and normalize our expression data.
We want to use Limma to analyze differential expression in this time
course experiment. W…
Dear all,
As a start I must confess that I am not really trained in bioinformatics. I managed to use bowtie2 and some samtools embedded in RStudio
updated 7.6 years ago • nginet
use the GUI functions.
I got the following error message
Error in shinytheme("readable") :
Valid themes are: .
My ChAMP version is 2.24.0.
How can I solve this problem?
Thanks for help
Hello ,
I want to collect a raw data or an expression dataset for breast cancer as a validation for my project. But I did not find within my purpose:
1) tumor-normal samples
2) affy
Is there anyone who used to
updated 10.0 years ago • libya.tahani
like a
common reference design for comparing the grous.
I suggest
agegroup <- factor(targets$Name)
design <- model.matrix(~0+agegroup)
colnames(design) <- levels(agegroup)
Then the three coefficients compare LTP to Control...the age groups, just extract contrasts
as
usual,
cont.matrix <- makeContrasts(YvsA=young-aged,levels=design)
and so on
Best wish…
updated 17.0 years ago • Gordon Smyth
The Thakurela Laboratory in the Department of Pediatrics and Lurie Center for Autism at Massachusetts General Hospital (MGH) and Harvard Medical School (HMS) is seeking exceptional candidates in Epigenomics at the postdoctoral level to direct projects involving investigation of neurodevelopment pathways and related neurological disorders.
The...Harvard Medical School (HMS) is seeking exceptional…
updated 3.1 years ago • sudhir.thakurela
lt;- targetsA2C(targets)
>u <- unique(targets2$Target)
>f <- factor(targets2$Target, levels=u)
>design <- model.matrix(~0+f)
>colnames(design) <- u
>corfit <- intraspotCorrelation(MAaq, design)
Here I'm getting...design, correlation=corfit$consensus)
"Error in if (abs(correlation) >= 1) stop("correlation must be
st…
updated 20.0 years ago • krasikov@science.uva.nl
both SKO1 and SKO2. The DKO sample expression can also be added in order to account for the basal levels of gene expression without the two stimuli; the differential "equation" thus becomes:
(WT+DKO) - (SKO1 + SKO2) = Synergy
*I am not...taking the average of SKO1 and SKO2 on purpose; to note synergistic effects, we must compare to an additive effect. I am specifically interested in the ge…
updated 6.5 years ago • Tima Karginov
gt; rownames(theData) <- basename(xys.files)
> vm <- data.frame(chanel = factor("_ALL_", levels = c("channel1",
"channel2", "_ALL_")), labelDescription = "oryza sativa")
> pd <- new("AnnotatedDataFrame", data = theData, varMetadata...dans validObject(out) :
invalid class "ExpressionFeatureSet" object:
'NChannelSet' varMetadata must have a 'channel' column
h…
updated 15.1 years ago • Michael MOZAR
to develop new bioinformatics methodologies for high throughput biological computing. The incumbent must have ability to collaborate on research projects and independently conduct analyses of big ‘omics data, primarily...of scientific workflows, algorithms and statistical analyses.
Design, develop, improve, test and validate complex bioinformatics workflows for production use in critical medical…
updated 4.0 years ago • Jenny Drnevich
<div class="preformatted">Dear all,
My apologies, the annotation problem was not with biomaRt, but with
the prepackaged datasets:
1. lumiHumanIDMapping.db and
2. lumiMouseIDMapping.db.
The description of the problem remains the same, though.
Gioulietta and Wolfgang, thank you for the prompt reply.
Regards,
Nenad
p.s. The missing sessionInfo():
R version 2.8.0 (2008-10-20)
i386-apple…
updated 16.8 years ago • Nenad Bartonicek
problem loading lumi package, Error : object ‘sqliteQuickSQL’ is not exported by 'namespace:RSQLite'
Hi All,
My name is Lucas, I'm currently doing an internship for my Master degree using Bioconductor to analyse the outcome of the HumanMethylation450...longer contains the function "sqliteQuickSQL".
So I removed the current version of RSQLite that I must have updated since October 25th, and reinstalled the previous version (0.11.4), and then tried to reinstall lumi again
updated 10.6 years ago • lucashusquin
end=10020)
#but then when I use start=full.df$Start. It naturally throws an error
saying 'start' must be a vector of integers
Questions:
How Do I handle this?
Does start here mean that each chromosome numbering starts from...1?
How do I split each sequence retrieved and create as fasta format
(>)with
sequence name attached to them retrieved from my input file?
>sessionInfo()
…
Hello,
I have created a plant list that I need to compile with the GenBank database to get thier accession numbers. I tried "ape" or "genbankr" package but I cannot find a suitable function that would enable me to do this.
For example i need to get accessions of these mosses:
"Abietinella abietina",
"Abietinella hystricosa",
"Acaulon muticum",
"Acaulon triquetrum",
"Aloina aloides"
messages:__
__1: In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
The 2 combined objects...have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)__
Then i treid next step that is…
updated 7.3 years ago • raya.girish
Using time-lapse microscopy I then track the motion of the cells of each type and at each dose level. I wish to see if cellular motility exhibits a dose dependence within cell lines and whether this putative positive...between dose and speed (say) can be explained by comparing protein (and gene) expression. The level of correlation between speed and dose is a continuous variable between -1 and 1.…
updated 5.2 years ago • justindean9208
Y Moreau et al.(2003) Trends in
Genetics(19)10:570-577.
3. "Meta-analysis of microarrays: Interstudy validation of gene
expression profiles reveals pathway dysregulation in prostate cancer."
D
Rhodes et al.(2002) Cancer Research...statistically allowed. or do i have to do some
> treatments for all 4 studes, to bring to a some level
> so that the expression values can be comparable. …
updated 20.8 years ago • Margaret Gardiner-Garden
the function ReadAffy. The error is reproduced here:
Error in validityMethod(object): No slot of name "phenoLabels" for
this
object of class "phenoData"
I don't know what's wrong. Any help appreciated.
thanks,
suresh
_________________________________________________________________
updated 22.1 years ago • James W. MacDonald
I want run deseq2 from tximport data. for sample dataset I can able to create deseq2 matrix file but for own data getting error i have kept same row(15) and column(15) name in condition and count data still getting error i have seen many already available question mentioned to update the versions after updating the version getting same error
please help
Thank you
```r
library(DESeq2…
<div class="preformatted">
Hmm..I forgot.
In our function we use the vennDiagram function which is a part of the
limma package. So U must have that package loaded.
/M
Hi.
At our department we have made a small vennDiagram script.
I am not sure if it suites your needs...I forgot.
In our function we use the vennDiagram function which is a part of the
limma package. So U must have that pack…
updated 21.6 years ago • Marcus
error :
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments.
It seems that this UNIPROT (verified
updated 8.2 years ago • julie.chevalier
library(affy);
pmindex(x)},
Dilution) # Returns a LIST!
all.equal(indexMaster, indexSlave[[1]])
[1] "Names: 40 string mismatches"
[2] "Component 12586: Numeric: lengths (69, 20) differ"
[3] "Component 12587: Mean relative difference: 1.345755
updated 17.6 years ago • Markus Schmidberger
for the levels other than the base
level. Expanded model matrices are described a bit in the man pages
and in the vignette, but not yet...an example with interaction
effects. This makes the DE analysis independent of the choice to base
level, whereas previously the log fold change (LFC) shrinkage was not
independent of base level choices. In addition, it simplifies...interaction terms, previously…
value = colnames(countData)) :
duplicate rownames not allowed</pre>
But when I test the row names for duplications I can't find any.
<pre>
> anyDuplicated(rownames(countdata))
[1] 0
> table(table(rownames(countdata)))
1
12402
updated 7.7 years ago • Assa Yeroslaviz
<div class="preformatted">Dear List,
I am using limma to analyze a gene expression microarray experiment,
similar to
the one described in the Monograph (Chapter 23.5: Technical
Replication, page 404):
a knock-out versus wt (BIO effect) 2-color mouse experiment, using
dye-swaps
(DYE effect) and two independent biological replicates (GROUP effect).
My problem is that I get a lot of differen…
updated 18.8 years ago • thama@imbb.forth.gr
letter and resume, to
include at least three contacts for references. All requested
information must be submitted for your application to be considered.
Please send academic transcript(s), to:
Rhonda Lipking, Administrative...mailto:vjongene@illinois.edu>, Phone:
1-217-244-1795
For full consideration, applications must be received by 5:00 pm April
13, 2012.
The University of Illinois is an E…
updated 13.7 years ago • Jenny Drnevich
gt; library(limma)
> gset38932 <- getGEO("GSE38932", GSEMatrix =TRUE)
> GPLid <- levels((gset38932[[1]])$platform_id)
> if (length(gset38932) > 1)
+ {
+ #idx <- grep("GPL5936", attr(gset38932, "names"))
+ idx <- grep(GPLid, attr...gset38932, "names"))
+ } else
+ {
+ idx <- 1
+ }
> gset38932 <- gset38932[[idx]]
&a…
updated 11.3 years ago • Guest User
function. Weights are a somewhat simplistic but general way of accounting for the varying noise levels between different observations in many types of data. I'm interested in developing generic approaches for things...other packages with support for weights, and what is their preferred representation?
* Would a naming convention for assays be a good way to do this? For example a "log2CPM" assa…
updated 6.9 years ago • Paul Harrison
just the samples that fit
a
threshold (that I have not set yet and may need help finding the right
level) for genotyping. It should be able to "no call" samples outside
the
clusters. It also needs to accommodate a negative control...any range of samples and
assays.
the data headings from the csv are:
ID,Assay,Allele Y,Allele
X,Name,Type,Auto,Confidence,Final,Converted,Allele
Y,Allele X
where A…
updated 13.5 years ago • Hans Thompson
Hi all,
I'm using Anaquin to measure detection of Sequin fold change by a sequencer. The fold change is between Sequin mixes A and B. When I try to make a ROC plot using the following parameters:
- Expected log fold change
- 1 minus P-value of measurement
- TP/FP label of measurement
plotROC collapses all the curves, each one representing a different level of fold change, into a singl…
<div class="preformatted">Hi,
I'm trying to use limma to analyze the following: Originally, there
were 6 arrays (3 biological reps, each with a dye-swap hybridization).
There was a technical issue with one of the arrays, leaving me with an
'unbalanced' design:
SlideNumber Name FileName Cy3 Cy5
1 PI-1_vs_DMSO-1 PI-1_vs_DMSO-1.txt PI DMSO
2 DMSO-2_vs_PI-2 DMS…
I'm running the RNA-seq gene-level workflow largely described by Mike Love (http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene...I'm running the RNA-seq gene-level workflow largely described by Mike Love (http://master.bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html). It had been running just fine, but yesterday the workflow s…
with trait data, but I have a large RNA-seq sampling but few trait data. I was wondering if it is valid do WGCNA just with the expression data and not including any trait data.
Thanks
whether a covariate is differentially expressed/abundant or not.
I wonder, if the same argument is valid, when the analysis is not performing any test but for example, regressing these genes over case/control. In this regression
updated 10.2 years ago • akp
10815 . + . ID=Os01g0100100;Name=Os01g0100100;Note=RabGAP/TBC domain containing protein. (Os01t0100100-01);Transcript variants=Os01t0100100-01
chr01...12435 . + . &…
updated 8.5 years ago • sancharisircar24
gt; label.perm <- label[permutation] # same permutation of labels
>
> k <- 5 #set cross validation steps
>
> for (i in 1:k){
+ win <- round(n/k) # size of window
+ cv <- ((i-1)*win+1):min(n,i*win) # move window
+
+ CV.label.test <- label.perm...object$scaled, drop = FALSE], center
=
object$x.scale$"scaled:center", :
length of 'cent…
updated 15.0 years ago • Zhe Liu
nbsp;GSEAGOHyperGParams, I run the hyperGTest function:
params <- GSEAGOHyperGParams(name="test",
geneSetCollection=mygsc,
 ...in getUniverseHelper(probes, datPkg, entrezIds) :&n…
1.6">So I had to run SortSam as well, which produced the error "Mapped mate should have reference name" the error that FixMateInformation was supposed to fix. So I went back and used MergeSamFiles with sort enabled, it worked...nbsp;
1. FixMateInformation was unable to fix the original problem, and MarkDuplicates did not validate beyond checking the flags which told it that read pairs had map…
updated 10.3 years ago • koustav.pal
Recent ...
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