want that is for the following: I have an IRangesList of
transcripts (describing exons at the genome level) and for every one,
I have a bp position at the transcript level that I want to convert
into a genomic bp position. Basically...as.integer(rng)[transcript.pos]).
I considered the IRanges approach because I keep the transcript name
and I'm sure that I looking up the right coord in the right
…
Order by: Relevance
function always returns the following error:
<pre>
Error in checkSlotAssignment(object, name, value) :
assignment of an object of class “GRangesList” is not valid for slot ‘rowRanges’ in an object of class “SingleCellExperiment
updated 8.1 years ago • Walter F. Baumann
mart)
I have modified the GeneRegion method such that it can work with
older,
hardcoded attribute names. It started to give error once again due to
"strand" not being one of the filters supported by old ensembl build.
Therefore...in listFilters(mart, what = "type") :
The function argument 'what' contains an invalid value: type
Valid are: name, description, options, fullDescription
I also tried …
in a way not unlike what's already been doing in \`clValid\`, which uses common cluster validity indexes to optimize k for \`cutree\`.
The problem is: dynamicTreeCut occasionally decides some genes as unclustable...i.e. cluster 0). For the calculation of validity indices, it is appropriate to also include these unassigned genes, or to remove them from the distance matrix from
updated 8.5 years ago • johnmcma
other hand for the same comparisons, glmLRT gives me a few hundred genes.
Is glmQLFTest not valid for multiple contrasts?
If I move forward with my analysis using the glmLRT function, will my results be valid?
Thank
updated 9.4 years ago • grastalt27
at time point x
* T2 ? U2
* T6 ? U6
* T12 ? U12
My problem is the following: Is it statistically valid to
estimate the interaction Time:Treatment using such an unconnected
design?
Using the following design matrix
T2vsU2...8,] 0 0 1
[9,] 0 0 -1
and contrast matrix?
Contrasts
Levels Interaction_6_and_2_hours Interaction_12_and_6_hours
…
updated 18.8 years ago • Serge Eifes
__The ____Computational Systems Pharmacology__ research group (<http://cosphar.utu.fi/>) led by Dr. Jing Tang focuses on developing and applying mathematical and computational tools to tackle biomedical questions that may potentially lead to breakthroughs in drug discovery, such as 1) how to identify drug combinations that can be used to provide more effective therapeutic strategies for can…
updated 9.5 years ago • jing.tang
code at the end of this message.
Therefore, I decided to leave the behavior as is for the low-level
HDF5
functions (upper case H5? functions and HDF5 object identifiers).
However, for the HDF5 high-level functions (lower...lt;- H5Fopen(hf)
> > h5dump(fid)
> named list()
>
>
> ## Now leave the rhdf5 handle open in the reader and go back to the
> ##…
readBin(con, dattype, n = (offsets["dataend"] -
offsets["datastart"] + :
'signed = FALSE' is only valid for integers of sizes 1 and 2
2: In readBin(con, dattype, n = (offsets["dataend"] -
offsets["datastart"] + :
'signed = FALSE' is only valid...readBin(con, dattype, n = (offsets["dataend"] -
offsets["datastart"] + :
'signed = FALSE' is only valid for integers of sizes 1 and 2
4: In read…
updated 14.1 years ago • Aric Gregson
experiments. Now I am trying to
find to over which genes these peaks overlap (and extract the gene
name).
I'm sure this should be pretty easy, but I am just starting with
bioconductor, so some concepts are still vague.
Here's what
the
densityplot to place the plots in the order of the files in the folder
> densityplot(factor(name, levels = unique(name)) ~`FL1-H`, data =
fs.trans[1:5])
Why can't I use this then to do the same with an xyplot?
>xyplot(factor(name, levels...order.
I get this error message:
Error in typeof(x) : object 'name' not found
Error in xyplot(factor(name, levels = unique(name)), `SSC-H` ~…
updated 16.5 years ago • Anja Schiel
<div class="preformatted">Hello Bernd and BioC people:
Writing empty character strings results in a C-level HDF5 error
starting in
rhdf5 2.8.0. See transcript below, under 2.8.0 (I am not attaching the
transcript under 2.7.3, where...class="preformatted">Hello Bernd and BioC people:
Writing empty character strings results in a C-level HDF5 error
starting in
rhdf5 2.8.0. See transcript …
updated 11.5 years ago • Brad Friedman
<div class="preformatted">Hi,
please apologize my ignorance, but:
I have the impression that limma is calculating the means
of M values by averaging them after adjusting the signs of the
values to the design matrix.
But shouldn't it be something like:
log2( sum(2^M)/ncol(M))
since these values are on a log 2 scale?
A second question is how do I specify contrasts when I would like
to have…
calling the interaction term would accomplish this, based on the vignettes:
results(dds, name = 'fungal_tr_Fungus1.soilmoistureD')
However, I am worried the interaction term will not account for the reference level...of the fungal_tr(Sterile_Control) for each soilmoisture level (W and D).
One last question I had was that **if** you can use the interaction term and it does account f…
Hello,
My name is Mahes Muniandy and I am a doctoral student working on twin data. I would like to compare the gene expression (Affymetrix...what I have.
<pre>
LG <- paste(targets$Gender, targets$LeanStatus, sep=".")
LG <- factor(LG, levels=c("F.O","F.L","M.O","M.L"))
Pairs <- factor(c("T1","T1","T2","T2","T3","T3","T4","T4","T5","T5","T6","T6","T7","T8",…
updated 9.9 years ago • mahes.muniandy
Hi,
I'm new to R, but am trying to analyze 2 ChIP-Seq data sets. I have been following along with several ChIPpeakAnno guides and I am running into a problem I can't figure out. I have managed to find overlapping peaks, but when I go to annotate them I run into the following problem:
> library(EnsDb.Hsapiens.v75)
Loading required package: ensembldb
Loading required package: Genomic…
updated 9.7 years ago • mhartman3
biomTrack,from=start,to=end,showId=TRUE)
Error in queryHits(findOverlaps(feathers, resize(levels[[cur.level]], :
error in evaluating the argument 'x' in selecting a method for function 'queryHits': Error in findOverlaps...feathers, resize(levels[[cur.level]], width = width(levels[[cur.level]]) - :
error in evaluating the argument 'subject' in selecting a method for function...findOverlap…
updated 11.1 years ago • Tiphaine Martin
span>
the model matrix is not full rank, so the model cannot be fit as specified.
Levels or combinations of levels without any samples have resulted in
column(s) of zeros in the model matrix.
As described
updated 10.5 years ago • catpowerb
using between group analysis with CA. It succeed to discriminate patients, but when I want to validate my model using the function of the package "bga.jackknife" which perform one leave out cross validation, the function
updated 9.0 years ago • crichard
to compare multiple gene lists, I
can't read the GO ontology terms on the graphic output because the
names run off the screen.
Also, when I plot a pie chart of GO terms at a high level, there are
too many GO terms on the pie chart and
BSgenome.Hsapiens.UCSC.hg19, vcfobj)
Error in .getOneSeqFromBSgenomeMultipleSequences(x, name, start, NA, width, :
sequence 1 not found
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no...sequence levels in common. (Use
suppressWarnings() to suppress this warning
updated 6.4 years ago • dfcarril
to load the data and I get this error.
#This is the warning I get.
Note: levels of factors in the design contain characters other than
letters, numbers, '_' and '.'. It is recommended (but not required) to...only letters, numbers, and delimiters '_' or '.', as these are safe characters
for column names in R. [This is a message, not an warning or error]
More Impor…
updated 7.0 years ago • evocanres
test
on these two data sets to see different outcomes for
two datsets on one pathway. Is this test valid only
for data in a 2X2 matrix, is this valid for a 2X12K
matrix (2 studies, 12K genes). I apologize if this is
a wrong question
updated 21.2 years ago • S Peri
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
However, I do not understand how to fill in the keytype argument. I see that "ENSEMBL" is not a valid keytype, so how would I go about this problem?
Seeing that "GENEID" is a valid keytype, I thought about doing the following...geneidSymbols```
and then using the Gene ID's as my keys in the new code. But "GENEID" is not a valid column type for org.Hs.eg.db, so that did not work either.
…
updated 6.7 years ago • kushshah
with plant genomics is desirable.
* Experience with phylogenetics software is also desirable.
* Must be prepared to travel internationally.
* Excellent communication skills in written & spoken English, and the
ability...interpersonal and communication skills,
with the ability to effectively interact with people at all levels in
a multi-cultural and multidisciplinary environment.
* Values …
updated 14.3 years ago • Sarah Ayling
run DMRcate with a dataset downloaded from a paper. This dataset consist, instead of a set of probe names and their corresponding beta values, of a set of genomic positions and their corresponding beta values.
When I run `cpg.annotate
updated 5.2 years ago • Jeni
<div class="preformatted">Hi,
I'm a PhD student from the University of Ghent, and I'm just starting
to learn how to work with R.
The initial aim is to analyse qPCR data with the package HTqPCR so I
read quite a few manuals regarding the program R and HTqPCR.
My problem is situated right at the beginning of the analysis, namely
loading my data.
I think I got it correctly that I first have t…
chr17', length(snps))
Error in validObject(.Object) :
invalid class "Seqinfo" object: 'seqnames(x)' must be an unnamed
character vector with no NAs
According to the man page this should be doable:
?`seqnames,GRanges-method`
seqnames...x), seqnames(x) <- value: Gets or sets the sequence
names.
value can be an Rle object, character vector, or factor.
# Try using an Rle…
and am fitting cell means models to test differences in treatment means and also fitting factor levels models to test main effects and interactions. I am finding that results for the tests for zero main effects give...lt;- model.matrix(~0+group) # cell means model
design.fl <- model.matrix(~f1*f2*f3) # factor levels model,
dat.new <- DGEList(counts=r.counts, group=gr…
Hello,
How can I figure out this?
Thanks in advance!
> head(huang\_group\_list)
x
1 549\_repair.bam
2 6\_repair.bam
3 …
updated 7.6 years ago • yueli7
targets$Tissue,sep="."))
> design <- model.matrix(~0+Treat)
> colnames(design) <- levels(Treat)
And then estimates subject correlation by setting a block by Subject:
> corfit <- duplicateCorrelation(eset
<div class="preformatted">
On 2/28/10 7:16 PM, "Tony Chiang" <tchiang at="" fhcrc.org=""> wrote:
> Hi Steffen et al,
>
> Quick question about a search query via biomaRt. Here is the code
that I am
> using:
>
> *****
> library(biomaRt)
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> filters = listFilte…
updated 15.8 years ago • Hotz, Hans-Rudolf
Hello everybody,
I am a student currenty trying to learn how to use clusterProfiler. I figured out a few things but I still have many issues, (I apologize, I know that usually its' better to ask only one question), since I also have a lack of knowledge in this field of biology.
First, I am not sure about the format of the input file : I'm trying with a txt file shaped like this :
Ensembl\_Gene…
updated 8.8 years ago • Mataivic
as a 2x4 factorial design. I'm interested in the interaction of parent treatment (group, levels: Control, Exposed) and development (stage, levels: 19, 28, 35, HA) on embryonic gene expression, and am trying to define a contrast...z$samples, combi=combi)
design2 <- model.matrix(~combi, data=z$samples)
colnames(design2) <- levels(combi)
colnames(design2) <- gsub("co…
updated 8.7 years ago • Jane Park
Embedded in the Boston Children’s Hospital / Harvard Medical School research community, the Sr. Bioinformatics Scientist will collaborate with pediatric researchers on a variety of projects ranging from translational and clinical research to basic science studies. Members of our community have varying levels of bioinformatics expertise and work on diverse disease areas including rare pediatric di…
updated 4.7 years ago • shira.rockowitz
limma)
\# limma
design <- model.matrix(~0 + eset\_filtered$cohort)
colnames(design) <- levels(eset\_filtered$cohort)
fit <- lmFit(eset\_filtered, design)
contrast.matrix <- makeContrasts("T12-T0","T24-T0",levels = design...make sure your column name is matched to cohort name
fit2 <- contrasts.fit(fit, contrast.matrix)
fit2 <- eBayes(f…
updated 8.2 years ago • pbachali
please help me out.
Here is the code that I run
```
# condition_pairs <- t(combn(levels(HB$Treatment), 2))
Error in combn(levels(HB$Treatment), 2) : n < m
# Here is my metadata named HB
Run collection_time Sample Name
updated 4.7 years ago • Rishav
them in the linear model for any other comparison I do. I
have a factor sampleType that has levels 1 to 4 and I am interested in
the comparisons 1 vs 2, 1 vs 3 and 1 vs 4. Is this a suitable way to
set up the design matrix:
design
updated 15.0 years ago • Daniel Brewer
IFNG.24
24 GSM23922 IFNG.24
> targets <- readTargets("Targets.txt")
# build factor of target names
> targetnames <- c(rep("C.1",4), rep("C.6",4), rep("C.24",4),
rep("IFNG.1",4), rep("IFNG.6",4), rep("IFNG.24",4))
> targetnames <- factor(targetnames...levels=c("C.1", "C.6", "C.24",
"IFNG.1", "IFNG.6", "IFNG.24"))
[1] C.1 C.1 C.1 C.1 C.6…
Having an issue with genotype.Illumina with crlmm
test <- genotype.Illumina(
sampleSheet=sampleSheet,
cdfName = 'humanomniexpexome8v1p1b')
I get this error:
Instantiate CNSet con…
updated 9.2 years ago • mcgaugheyd
Dear all,
in short, I would like to decide whether a certain data set contains
sub-groups (clusters), or is uniform.
There are roughly 500 features and 50 samples. I am looking for
clusters of samples.
There is a clear division in a small number of features (3-4)
indicating the existence of subgroups, and a much less clear situation
in many other features. Pvclust, which I use preferentially (…
x <- as.matrix(x)
> batch <- as.factor(batch)
> contrasts(batch) <- contr.sum(levels(batch))
> if (is.null(batch2)) {
> X <- model.matrix(~batch)[, -1, drop = FALSE]
> }
> else {
> batch2 <- as.factor(batch2)
> contrasts...batch2) <- contr.sum(levels(batch2))
&…
updated 5.1 years ago • Gordon Smyth
I have this function and sometimes it gives me error:
<code>refGenes <- UcscTrack(track="RefSeq Genes",<br/>
table="refGene",<br/>
 …
logCPM, I get the following error message:
Error in array(x, c(length(x), 1L), if (!is.null(names(x))) list(names(x), :
'data' must be of a vector type, was 'NULL'
Thanks a lot in advance,
pavlos
updated 10.2 years ago • pavlidisp
<div class="preformatted">Hello****
I am trying to use rtracklayer and specifically UCSCTableQuery to
retrieve
information from UCSC tables but I want to retrieve the information
only
on certain genomic segments. ****
** **
In the following example I try to create a UCSCTableQuery that will
return
A GRanges of the tRNAs in a set of given ranges, defined by a GRanges
object . Specificall…
updated 13.3 years ago • d r
error message:
>
> > as("myArrayLM", def);
>Error in methodsPackageMetaName("C", name) :
> 'The name of the object (e.g,. a class or generic function) to
>find in the meta-data' must be a single string (got an object
function(x){sum(width(reduce(x)))})
exonic.gene.lengths <- as.numeric(exonic.gene.sizes)
names(exonic.gene.lengths) <- names(exonic.gene.sizes)
summary(exonic.gene.lengths)
\# Min. 1st Qu. Median ...values are less than the average fragment length of 134 (for one sample). So something must be going wrong here. So the effect…
updated 7.5 years ago • Ina Hoeschele
I have a simple2x2 design for RNASeq DEG analysis with DESqe2. When I read the manual I got quite confused by the examples provided for the two conditions,two group design.
I. by doing the following, are we trying to find genes expression level differences between conditions A and B or between group Y and X?
" results(dds, contrast=c("condition","B","A")) "
2. By…
I'm running goseq on a sequence of bootstraps where a DE test is performed on a random selection of replicates. THis way, I have a constant list of background genes and a selection of significant genes which is slightly changing from bootstrap to bootstrap. goseq works nicely on most of these bootstraps, but every now and then it crashes. Here is an example:
<pre>
> library(goseq)
…
updated 10.8 years ago • M.Gierlinski
to generate "dataset" for down-stream of DESeq2.My question is, how can I make interested column names ("i") to be recognized as a variable in design = ~i or something similar to this concept?
DEG_analysis <- function(i)
{
colData_tmp...Error in DESeqDataSet(se, design = design, ignoreRank) :
all variables in design formula must be columns in colData
updated 5.4 years ago • rekren
<div class="preformatted">Hi,
This email is just to notify the users of lumi package and Illumina ID
mapping packages. To be better compatible with the naming convention
of
Bioconductor annotation packages, we renamed the Illumina ID mapping
packages by removing the ".db" suffix...notify the users of lumi package and Illumina ID
mapping packages. To be better compatible with the naming con…
updated 17.1 years ago • Pan Du
gt;
>
> - If I have data with three factors: condition, age and
group.
>
> The levels of condition are: treated and untreated
>
> The levels of age are: young and adult
>
> The levels of group are: 1 and 2...gt;
> I had an idea to combine the factor age and condition into one
factor: age_condition (with levels young_treated, …
updated 11.6 years ago • Michael Love
an advantage. Prior experience in genomic or proteomics research is not essential, but the applicant must be highly motivated to work on problems in medical biology.
**Terms of appointment**
This position will be available for...2 years in a full-time capacity. Salary is Academic Level A (AUD90,053 - 96,661 per year, dependent upon qualifications and experience) for Research Officer, and Ac…
updated 5.9 years ago • Gordon Smyth
RowSideColors* - I am also trying to use a
specific column of my dataframe, which has 6 different levels of
annotation,
to plot RowSideColors - I was able to do this:
x <http: hct.delta.body.ma=""></http:> <- y[,c(3,9:10)] # 3 is the column with...the
levels of interest - for coloring - and is labeled "USCS"
z <http: hct.delta.ma=""></http:>.ma <- as.matrix…
updated 14.1 years ago • Kurinji Pandiyan
to create a densityplot:
Error in apply(xx, 2, function(y) all(sign(diff(y)) >= 0)) :
dim(X) must have a positive length
until i finally found out that this error is thrown by the
flowCore:::findTimeChannel function...function for flowSets, since this
function will
always result in an error if there is no column named Time.
I finally realized that by calling densityplot and specifying …
0 Up NaN NaN</pre>
I think this might be due to gene names of the statistic getting stripped away inside the function by as.numeric(). Simple fix - If I make the following change...lt;- as.numeric(statistic)
G <- length(Stat)
<span style="background-color:Yellow"># ID <- names(Stat) # Replace Stat with statistic which still has names
ID &…
look for transcription factor binding motifs that are disproportionately represented in the list of named genes above background levels. As others have described, I am finding this software to be a bit buggy and would much rather
updated 7.9 years ago • JMallory
genes have been placed in more than one
spot. What I would like is to do is to group spots by gene names in
MA$genes and calculate the average logratio as the expression level
(better still, ignore the spots with zero weight
updated 20.1 years ago • alex lam RI
May
someone let me know where I could find a .CSV file that includes both
Probe
Set IDs and gene names for this array?
Thanks,
Shery</div
REACTOMEID")
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.
> select(reactome.db, keys = genes.id...REACTOMEID")
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 l…
updated 9.0 years ago • Lluís Revilla Sancho
Recent ...
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