Hi,
It seems to me the reactome.db package is based on human content of
the Reactome database (Entrez identifiers, mappings to GO, etc). I
would be delighted to see support added for other organisms
(especially for mouse
Order by: Relevance
How can do this with goProfiles, I already have GO terms and I can
easily do the profiles using entrez ids doesn't work with GO.
I would appreciate for help.
Best!
-- output of sessionInfo():
a
--
Sent via the guest posting facility
updated 13.3 years ago • Guest User
Hey! I'm doing some analyses with Limma. I have 5 cluster and I want to find genes up and down regulate in the first one versus the others 4, to identify the ones that are typical of this cluster.
```r
mm <...Hey! I'm doing some analyses with Limma. I have 5 cluster and I want to find genes up and down regulate in the first one versus the others 4, to identify the ones that are typical…
updated 2.1 years ago • michelafrancesconi8
div class="preformatted">Dear all,
i have a question for you.
If i have a list of 66 genes:
> SHR
ExpressionSet (storageMode: lockedEnvironment)
assayData: 66 features, 4 samples
element names: exprs
phenoData...none
experimentData: use 'experimentData(object)'
Annotation: rat2302
and i would found which genes are involved in the "hypertrophy" and
"cardiac decompensation" pathways.
…
div class="preformatted">Dear bioconductor-users,
I'm looking for a way to query the gene ontology in R like in the GO
browser (AmiGO). I tried different packages (NCBI2R, GOsim ...) but I
did not find a simple way to extract...genes names associated to a GO
term (i.e. myelination). Could you tell me if there is a way to do
that?
Thanks,
Hervé
`·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·.¸¸.·´´¯``·…
chromosome location (org.Hs.egCHRLOC) and end position(using
org.Hs.egCHRLOCEND) of a list of gene symbols. But I did not find
which one mapped the gene length to its symbol. Should I subtract what
I get in org.Hs.egCHRLOCEND...from org.Hs.egCHRLOC for each gene symbol
to find the gene length or is there an easier way to find it for a
long list of gene symbols.
Thank you</div
updated 13.3 years ago • Fatemehsadat Seyednasrollah
div class="preformatted">I have performed the gene selection and now what GOstats should do? As
I
know I should define the gene universe. Is it possible to use such
code?
b<
Hi,
I used WGCNA for finding modules. I found 9 modules: turquoise(1501), red(173), pink(41), magenta(36), grey(6), green(446), brown(348), blue(382),black(67). Based on Univariate Cox Model just turquoise is significance. The number of 1501 genes in turquoise module is high and I have to filter more for Gene Enrichment Analysis (GEA) and finding significant pathway. So, how can I decrease th…
Hi, I'm using featureCounts from the Rsubread package. But I have a question about the gene length returned by featrureCounts.
I've read the case study here: <a href="http://bioinf.wehi.edu.au/RNAseqCaseStudy/" target...from a RNAseq experiment, and I just used the rpkm() function in edgeR. This function takes the gene length as input, which I got by featureCounts. So I wonder __how feature…
updated 9.3 years ago • niuyw
div class="preformatted">if i have only one sample, how can i say
if a gene expression are upregulated significantly or not?
how can i set a standard? using some public data
to get an average level...of gene expression or set a
reference gene level,like actin?
--
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute for Plant Research
updated 12.8 years ago • wang peter
Xiaowei Guan wrote:
> Dear Bioconudctor,
>
> I have this question about how to compress the gene expression
dataset from
> probe sets denoted to gene denoted values.
>
> The analysis has two simultaneous goals, first...is to convert the
probe sets
> to gene names. Second is to convert the probe sets values into just
one
> summary gene expres…
p/354073/#354353) and then I got the answer that I should use deseq2 normalization with gene length adjustment. Is it possible to use deseq2 normalization with gene length adjustment like as FPKM gene length adjustment...I have 250 samples from healthy and disease states and I want to integrate gene expression with metabolic model. Indeed, I need within sample normalization (adjusting gene length…
updated 7.1 years ago • Maryam
Wondering about the most straightforward way to take a list of genes and create a GRanges object, so basically pull the intervals for lets say a list of 500 RefSeq genes? Thanks
updated 8.0 years ago • rbronste
Dear all,
after clustering a gene expression dataset, please can you advise, how can i extract the group of gene names corresponding to the dendrogram
updated 8.9 years ago • Bogdan
I've been trying to run GSVA and have come across the warning message below. I actually have no genes where all samples have constant expression values. It looks like this warning is being caused by genes with partial...0. The NA values are a result of combining multiple different microarray and RNA-seq datasets. Any gene that has one or more NA value is being removed from the analysis, some of …
updated 3.7 years ago • blakebowen
Hi,
I used both gage package in R and GSEA software for KEGG pathway analysis and since the 2 tools have different algorithms, I got slightly different results in the list of genesets. I was able to find the genes in each gene set from GSEA from their website, but I don't seem to find the gene list of some gene sets that I got as a result of GAGE analysis on GSEA website. A couple of those are:
…
updated 8.4 years ago • sup230
A.
I already had a count table, and would like to use rpkm() in edgeR, but first I have to get a gene length vector. My question is how to count gene length from an "Ensembl.gtf" file by taking into account the following:
1...Gene 1 is much longer than Gene 2 if including both exon and intron. But Gene 1 only has 3 exons, and Gene 2 has 10 exons --> for the...transcripts, Gene2>Ge…
Hello!!!
I’m running Deseq2 to find differentially expressed genes in breast cancer samples according to genetic ancestry. For this I categorized my samples in three groups according...samples), G2: 50-75% (35 samples), G3 (6 samples): 75-100%). Running these comparisons I found some genes the problem is that when I create just two groups, none gene appeared, why this could happen? I could be …
class="preformatted">Dear all,
I have been using the bioMart and DAVIDQuery R-packages to convert
gene identifiers into different formats. Unfortunately, both of these
packages require direct internet access for every...conversion.
Is anybody aware of an R-package or script which supports "offline"
gene name conversion, i.e. based on previously downloaded gene name
database files (disk space …
updated 16.0 years ago • Rainer Tischler
div class="preformatted">I have gene file in this format, everything in one column (no spaces
at all):
SFTPB|NM_000542.1|4506904|surfactant, pulmonary-associated
div class="preformatted">Dear all,
I have a script that generates a large number of gene sets (vectors of
gene names) and would like to apply a functional analysis (e.g. how
many transcription factors occur in...each gene set? how many kinases...
etc.). I can convert the gene names into different formats using
biomaRt, however, the only functional...analysis tools I have found in R
apply an e…
updated 15.8 years ago • Rainer Tischler
Do you know how to retrieve the genes corresponding to the proportions of up-/down-regulated genes reported in the mroast() output withinthe limma package
updated 9.1 years ago • rea
and tximport() functions, I can't find how to set a minimum number of reads per gene, which is necessary for correction of batch effects and recommended for differential expression.
How can I filter genes
updated 8.9 years ago • Peter Alto
<div class="preformatted">Hello,
I would like to plot a list of interesting genes (located on different
chromosomes) on a genome. I extracted their genomic coordinates with
biomaRt (see table below) and...div class="preformatted">Hello,
I would like to plot a list of interesting genes (located on different
chromosomes) on a genome. I extracted their genomic coordinates with
biomaRt (se…
updated 16.2 years ago • Jarek Bryk
to deal with count values, I was wondering if it could be applied to roughly detect differences in gene counts in gene families of two groups,
for example (numbers below represent counts):
![Mock matrix][1]
I'm assuming that each...species in such matrix could be considered a replicate within each group, that gene families would be the equivalent to loci, and counts are absolute.
Any su…
updated 3.7 years ago • eliza_3176
Hello! I was looking for a way to access a pathway in WikiPathways and to color some genes according to the log2FC I got from a differential expression analysis (much like pathview does with KEGG pathways...Hello! I was looking for a way to access a pathway in WikiPathways and to color some genes according to the log2FC I got from a differential expression analysis (much like pathview does with K…
updated 5.1 years ago • Emilia
is not the right place to ask, please advise.
The aim of my experiment is to look at healthy ageing gene expression changes. Thus, I want all of the data sets from GEO that studied gene expression at different ages (either comparing...data set.
6.
The GDS\_full.soft files have all of the probes (ID\_ref) and the Entrez Gene Name (GeneID). Make an excel sheet with three colu…
updated 7.0 years ago • StephK
p/9155447/
I'm wondering:
With limma::voom, we always filtered out lowly-expressed genes (typically using edgeR::filterByExpr) beforehand, because voom did not work well for low-count genes (and also because...voomLmFit, which can actually handle low counts, could we actually filter out much less, e.g. only genes that have no counts at all?
I am aware that prefiltering reduces the multip…
updated 2.1 years ago • annikagable
<div class="preformatted">Hello,
I would like to test the significance of GO terms using ANOVA. Correct
me if I'm wrong, but I think that it makes sense to make a three
factorial ANOVA (where genes are one factor, the experimental group
is the other, and the specific sample is the third) on a group of
selected genes (for example, group of genes belonging to a given GO
annotation group).
…
I have encountered something really confusing when I did my LRT analyses. I'm interested in gene P's effect on cellular immune reactions. In experiments, we treated the WT and P KO cells with either normal media (control...RNAseq experiments on these WT and KO cells.
Biological question: for a given treatment, which genes are differentially expressed in WT, that do not change expression in P …
updated 3.5 years ago • meeta.mistry
I am doing a candidate gene study with `DEXSeq v1.36.0` and would like to calculate test statistics for a single gene.
When running the code
```r
dxd.cand...na.rm, dims = dims, ...) :
'x' must be an array of at least two dimensions
```
For two or more genes it works fine. Is this a bug or can a gene Q value not be calculated for a single gene?
</gene_xy
updated 4.6 years ago • Matthias Munz
Which are the available packages in Bioconductor to quantify gene isoforms?
TIA
updated 6.4 years ago • angel.campos
<div class="preformatted">Hi List,
I am analyzing my RNA-Seq data with edgeR. The next is my experimental
design:
d.GLM
An object of class "DGEList"
$samples
group lib.size norm.factors
R4.Hot HotAdaptedHot 17409289 0.9881635
R5.Hot HotAdaptedHot 17642552 1.0818144
R9.Hot ColdAdaptedHot 20010974 0.8621807
R10.Hot ColdAdaptedHot 14064143 0.893279…
I am using the object types 'GeneSet' and 'GeneSetCollection' from the {GSEABase} package for my gene set enrichment analyses. One of the GeneSetCollections I am working heavily with I have setup from the downloaded gmt...file containing the latest release of the Molecular Signatures Database MSigDB.v.7.1 (gene symbol annotation based on Gencode release 33). I am wondering whether there was an ea…
updated 5.7 years ago • rocanja
Hi
My supervisor keeps telling me we should just use the p nominal genes from DE with limma as we don't get any FDR corrected ones. However if we do this, how do we know we are not just looking at gene
updated 9.8 years ago • chris86
sample from peripheral blood using microarray). Two conditions don't have differential express genes. But changes may be subtle at the gene level but more pronounced when looking at coordinated changes across sets of genes...within pathways. So I tried gene set variation analysis. Robert (the creator of GSVA tool which I tried on my data) suggested me using fgsea because my data...doesn't have di…
updated 20 months ago • Chris
<div class="preformatted">Hi, Is there a utility in BioC to retrieve data sets in NCBI GEO? Will
the
EFetch in Entrez do the job? Parsing something like this is not a big
deal,
but I would like to have a cup of coffee instead. Thanks! -Simon
http...preformatted">Hi, Is there a utility in BioC to retrieve data sets in NCBI GEO? Will
the
EFetch in Entrez do the job? Parsing something like …
updated 20.1 years ago • Simon Lin
in json text
<html> <head><title>504 Gatewa"
This happens only for a very small proportion of genes. It happens both when I either feed it a vector of gene symbols or when I manually write out the individual problematic...genes, as done below for "NFE2L2". When I fill in this gene in the online DGIdb, the gene exists and produces output.
Any idea what...s happening here and …
updated 21 months ago • Dennis
div class="preformatted">Dear List I've a generic question about Gene 1.0St arrays not strictly
related to bioconductor analysis.
I'm new to Gene 1.0 St chips.
Utilizing oneChannelGUi I've...expression
(GCRMA) for
my probesets.
With biomart each probeset was remapped to the corresponding gene
Now : In order to obtain the global gene expression is it sufficient
to
compute the median of the e…
updated 14.0 years ago • Guido Leoni
Dear community,
I am analyzing microarray data of patients followed from birth up to an age of 3 years. The samples were taken at various age points for each child.
I want to identify non constant gene expression over time within these children, so genes that are differentially expressed over time.
For this I have applied a mixed effects model with splines(df=3) in limma adjusting for se…
updated 2.4 years ago • triZZla
Hi~
I am working on RNA-seq data to evaluate the genes changing with age in different regions. My coldata looks like:
```R
> coldata
tissue age sex
1 PFC 3month female
2 Amy 3month...I would like to calculate the R-squared associated with the age-related variance for each genes in these two regions. But I am not sure how to evaluate age-related variance (the variabl…
<div class="preformatted">Dear Bioconductors,
Now my problem is as follows:
First of all, I read the microarray .gpr files to RGlist, then
normalized it to MAlist. After that I convert the MAlist to exprSet
for
further analysis. Now, I want to filter genes in exprSet according to
the names or probeID, but I found there is no geneNames Slot for my
exprSet. How to find or keep the...it to MA…
updated 19.4 years ago • yanju@liacs.nl
annotation of probesets in affy
GeneChips. I find that some times 2 probe sets refer to the same gene.
For example, in the HG_U95Av2, there are 2 probesets (1369_s_at and
35372_r_at) both point to the same gene IL8. I wonder what...What is then the point of having 2 probe sets which might
give different results for the same gene?
Please send any pointers/references that you find appropriate.
T…
updated 19.7 years ago • Saroj Mohapatra
Hi All,
I will like your advice in how to present the DE genes in a heatmap. I will like to show around 40 genes of interest, their log2FC varies between -1.3 to 5.4, but most of them...range between -1 to 1. One gene can be DE (FDR<0.05) in one but not all the datasets and I want to show this in the heatmap. But not sure how to deal with them
div class="preformatted">Hi All,
I am using RNA-seq to study the expression levels of gene globally and
as
well as group of genes. Plotsmear have given me a meaningful
information. I
believe the estimated norm.factor...values themselves are not modified. My question is if I
want to
check compare the expression between genes (within a group) what
values do I
need to consider for this analysis. …
updated 15.0 years ago • Sridhara Gupta Kunjeti
How to get gene names for the probe id's using
<pre>
pd.hta.2.0?</pre
updated 7.3 years ago • sunandinisharma
I'm trying to read the data of GSE81608 from GEO, but I can't see the gene names. I tried both by reading the CSV file, and by using GOEquery from R. It looks like the gene names are not available. (the...CSV just marks the genes by a running number) Is it possible that the dataset was published without the gene names? or am I missing something
updated 8.5 years ago • yuvallb
Hello
I have a coexpression network, and I have found the clusters of the gene of it using two different methods. Now I want to compare these two methods with each other with respect to the gene ontology
updated 6.5 years ago • na396
div class="preformatted">Dear Limma users,
In our study we would like to identify tissue specific genes, i.e.,
genes that are differentially
expressed in a specific tissue. From practical reason each RNA extract
is a mixture...expect to get a matrix of
expression
values for each gene, which like design matrix rows are RNA samples
and
columns are tissues. Where the observed value of LER mixture…
When I was analysing the output for the comparisons I noticed several instances where a gene was called DE despite intuitively seeming like the counts/number of samples with non-zero counts was too low. This included...several instances where a gene had literally zero counts in both of the compared samples (bearing in mind the 0.5 pseudocount from `plotCounts`):
```r
$ res...MUUL2 0.5 MUUL
MU…
updated 3.6 years ago • pt
When I use summarizeVariants with a GRangesList of genes, the genes are then reordered in the RangedSummarizedExperiment object and the assay(counts) values are incorrect...a bug or can I control this reordering?
<pre>
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
genes <- genes(txdb)
# get the gene symbol for corresponding ENTREZID
gene.map &a…
updated 8.6 years ago • Todd Creasy
package and noticed that there are some exons, that do not seem to be a part of any gene.
<pre>
> # get all the genes
> genic.regions <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
> # get all the exons
> exonic.regions...lt;- exons(TxDb.Hsapiens.UCSC.hg19.knownGene)
> # Find the overlaps between the genes and exons
> findOverlaps(genic.r…
updated 10.0 years ago • Aliaksei Holik
I am trying to annotate my Illumina data with more updated annotations than the manifest file from Illumina. I have thus tried the IlluminaHumanv3.db, but I get a lot of inconsistent results and are confused about what annotations to use. For example: The probe ILMN\_1736007 have no annotation using the illuminaHumanv3SYMBOL or illuminaHumanv3ENTREZID. However…
updated 8.7 years ago • christina.fjeldbo
package. The package named "ipihs324" has annotation for IPI
identifiers
and contains mappings to Entrez ids in the environment variable
ipihs324ENTREZID.
Now when I provide this environment directly like :
l <- mget("IPI00000948...As I want to write a generic code for loading any data package and
then
retrieve its environment for Entrez ids mappings, so I need to do it
this second way. C…
updated 18.1 years ago • Chanchal Kumar
I would like to limit the number of displayed genes (so **not** the categories, which is easily done with showCategory) in the enrichplot heatplot, but have not found a way to...I would like to limit the number of displayed genes (so **not** the categories, which is easily done with showCategory) in the enrichplot heatplot, but have not found a way to do...it. I am running the gseGO Function to…
updated 3.0 years ago • Melanie
and currently working on the identification of DEGs from a raw data which has about 50 thousand genes and after applying statistics on that I have come up with about 250 genes but the problem is that, the DEGs which have been...identified by using packages of bioconductor miss some significant and known genes which cause that particular disease. Now the question in my mind is that how to justify …
updated 5.9 years ago • nia
Hello Forum,
<span style="line-height:1.6">I want to perform gene set enrichment analysis of whole genome. Can it be done or I have to have some selective genes? Thanks for any input
and featureCounts to get expression values. I would like to counts the number of reads map to the genes and outside of genes. Is there any tool or script to get these estimates?
Thanks
updated 9.6 years ago • myprogramming2016
First, my apologies if this has been covered already. I thought for sure it would have been, but I can't find the relevant info with my searches.
It's pretty obvious from the DESeq2 vignette how to test whether a gene is differentially expressed (DE) and how to do so at various LFC thresholds, but what if I want to determine which genes are not DE? Is there a way to tease apart the genes for …
Input file is the list of gene ids along with fold change values:
```
14 1.23
43 -1.18
52 1.42
90 -1.2
212 1.42
291 -1.11
337 1.29
351 -1.31
358 1.19
372 -1.5
411 -1.43...1.13
471 -1.24
585 -1.46
596 -1.47
607 -1.47
632 1.37
```
Column one is gene id and column 2 is fold change
Code having error is:
```…
updated 5.2 years ago • Safina
Recent ...
Replies
Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
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ja569116
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0
Hi @atpoint Thanks for the information.
Could you please expand on when to use adjusted p-values vs nominal p-values.
My understanding was …
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It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
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The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
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I updated the above answer today.
Answer: When to use edgeR or limma
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68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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