of my LFQ-based proteomics dataset. I ended with a data frame containing the significantly expressed genes (in this case from yeast), their UniprotIDs, p-values, Log2(FC), etc. I would like, however, to add some annotations into my analysis
Order by: Relevance
div class="preformatted">Hi list,
I wonder, for gene expression analysis, would it possibe (in the
future) ,
using a bioconductor package,
that I supply a list of genes of interest...with gene expression values
and
fold change (condition 1 vs. condition2)
and then calculate the scores of this gene signature in
updated 17.6 years ago • affy snp
the
Affymetrix web site (Version 29 according to my notes).
It occasionally contains more than one gene per probeset separated by
3 slashes. For example for the probeset
1415691_at the genes listed are Dlg1 /// LOC100047603...Presumably this
is because the probeset is found to have
specificity for more than one gene.
When I get the annotation from mouse4302.db (version 2.2.11)
using
the…
updated 15.8 years ago • Richard Friedman
<div class="preformatted">Dear All,
I have RNA-seq data for 20 bumblebee samples divided into treatment
and control. I am interested in differential exon usage. Unfortunately
the bumblebee genome is not at the stage where I can do a complete
DEXSeq analysis genome wide. I decided to look at a single gene where
I have a decent gene model. Using TopHat2 and the python scripts
included in DEXS…
as.character(lookUp(ID, annodb, "SYMBOL"))
Name <- as.character(lookUp(ID, annodb, "GENENAME"))
Entrez <- as.character(lookUp(ID, annodb, "ENTREZID"))
Ensembl <- as.character(lookUp(ID, annodb, "ENSEMBL"))
annot = data.frame("ID...ID,"Symbol"=Symbol,"Description"=Name,"EntrezI
D"=Entrez,"EnsemblID"=Ensembl)
length(which(Symbol != "NA")) # 23672 =====> is this norma…
updated 11.6 years ago • Guest User
i am tryn to analysize RNAseq data by Kallisto to get the gene read count. after I get them, how can I reach to the gene I want? because it wont give me the every name of the gene, right?
would
updated 2.2 years ago • Gülsüm
issue concerning the TCGA RNAseq data provided on the Recount2 website.
Briefly, we would need of gene counts of a particular gene for the same set of TCGA individuals provided as RangedSummarizedExperiment objects. The...issue concerning this is that the gene is not annotated yet in the Ensembl/Gencode database (it's the gene of a novel lncRNA) , thus it's not possibile to find it across...raw …
updated 6.8 years ago • francesco.gandolfi
I am using Limma/edgeR packages for analysing my RNA-seq data from two bacteria. I am going to do Gene ontology analysis on the data. There is no built-in package for the two bacteria that I work on, so I made organism packages...The problem is, the packages made this way do not contain 'egGO2ALLEGS', so it is impossible to do gene otology analysis using gonna() function from edgeR. Does anybody …
updated 5.8 years ago • babak.loghmani
How are feasible genes selected in topGO. I can't seem to find any information on this? Many genes that are non considered feasible seem no different...that any other genes and their GO annotation?
Thanks,
Mike 
updated 8.9 years ago • michael.steffen
and have a basic question regarding probe sets.
so, why are there multiple probes with the same gene? Some probe sets have only one(and the same gene), if it's exactly the same gene what benefit does it provide us?
Thanks in advance
<div class="preformatted">Hello,
I am trying to get human and mouse homologs from worm genes. I am
querying wormbase using biomaRt.
I get an error when trying to use the 'gene' dataset (example below).
The other datasets work fine. Is there a way around this?
Thanks
Giovanni
library(biomaRt)
Loading required package: XML
Loading required package: RCurl
mart<-useMart("wormbase")
lis…
class="preformatted">
Dear Bioconductorians,
I am trying to find a suitable package to implement gene shaving. the
gene clust package looks very confusing. Is there any package that can
be downloaded and installed like any...other bioconductor package to
implement gene shaving?or can anybody help me with the instalation and
maual/tutorial of a workable r version of gene clust. i know there
updated 16.5 years ago • fire1976 wyoming
research interest, the data I am planning to work on is qPCR data, with much smaller number of genes (from around 30 genes), with relatively big sample size (1000 samples, highly heterogeneous). Apparently I could not...scale free topology, and identifying any big module, which I think is because of the small number of genes. I looked up a lot but could not find anyone asking ab…
updated 9.0 years ago • zson3366
for evaluation of qPCR data and it works fine with the default settings.
Is it possible to use gene specific efficiencies? In the vingnette it is mentioned that it is possible to use them but I have no clue where to change...the default parameter thatsets equal gene efficiencies for all genes.
Where can I change paramerters
updated 5.9 years ago • bettenbrock
data using limma. I would
like to
perform a cluster analysis after selecting the differentially genes
based on
the P value (say 0.001). As far as my knowledge is concerned I have to
do
the sub setting of these selected genes on
Hello,
I performed an analysis of differential expression with SAM method, obtaining the genes that are up and down. I used these scripts:
<pre>
> samfit = SAM(exprdc, group, resp.type="Two class unpaired", fdr.output=.01...Hello,
I performed an analysis of differential expression with SAM method, obtaining the genes that are up and down. I used these scripts:…
updated 10.5 years ago • santi.cabellos
I'm struggling with co-expression analysis, and for that I would like
to try to cluster all the genes I have in my microarray set, including
those which are not differentially expressed between the study groups.
I am using...my luck with GSCA as
well, but both packages seem to have been layed out for 3000 rather
than 30000 genes.
How do you do that in R? I get errors about R not being able to
al…
updated 14.4 years ago • January Weiner
no significantly differentially expressed genes. `logFC` are symmetrically distributed around 0 and range from `-1.5` to `1.5`. The `adj.P.val` ranges from `0.2` to `1` (vast majority...is `1`).
Nonethless, I decided to run `clusterProfiler::GSEA` (using hallmark gene sets from msigdb). For that I ranked the all genes according to the `logFC` that I got from running the differential gene express…
updated 3.8 years ago • nhaus
I recently run into the problem that the gene annotation in MSigDB is not up to date (for example, the alias C14orf129 is used as a gene name in various gene sets, while...symbol
# DUX4L DUX4
# DUX4L LOC112268343
indices <- NULL
for (gene in setdiff(duplicated.aliases, aliasSymbol$symbol)) {
tmp.index <- which(aliasSymbol$alias_symbol == gene)
ali…
updated 7.6 years ago • t.kuilman
the baseMean, log2 fold change, and pvalues, except that the rows are numbered rather than named by gene.
I would assume that the genes are listed in the same order that they appeared in the countData, ie I could annotate the results...file with gene names by simply assigning it the countData row names. I hesitate to do this, however, in case some other ordering occurred...entirely des…
updated 8.5 years ago • kalaga
div class="preformatted">how to combine transcripts of one gene
i have a fasta file which have many transcripts
i want to cluster those transcripts to the gene level
without the reference
updated 13.9 years ago • wang peter
div class="preformatted">Are there tools available for differential gene set analysis?
e.g., if I apply the same treatment to two different cell lines,
and find gene sets that are enriched in each...with respect
to untreated, can I compare the lists of gene sets and
find ones that are significantly enriched in one but not
the other?
</div
updated 13.8 years ago • Ed Siefker
Hi,
Is there a way in SingleR to know for each cell in the test data- which genes (in the test cell) are mostly correlated with the genes in the predicted cell from the reference dataset? For example, for...X in test data that is predicted to be cell Y in the reference data - what are the highly correlated genes in X with Y?
Thanks!
Liron
updated 5.4 years ago • lirongrossmann
to a drug (measured by CellTiter-Glo assay). I have sourced a counts matrix with corresponding basal gene expression for matching cell lines with over 50,000 protein coding and non-protein coding genes [here][1]. I would like to...code without pre-filtering, and plotting counts of my most significantly differentially expressed genes (ordered by adjusted p-value):
```R
plt = plotCounts(deseq_ds, g…
Regarding the approach to classify tumor samples to subtypes based on different gene sets with gene expression data, my question is: what is the significance of the approach when not all the genes of the gene
div class="preformatted">Dear List,
I'm new to microarray analysis and need to calculate gene signal from
samples. The tab-delimited file has been prepared and the signal for
each
probe is calculated. My question...is: 1) How to filter the probes those
are
disqualified? 2) How to calculate the gene signal from probe signal?
The
reflection from probes to genes are clear but I have no idea if I…
updated 15.6 years ago • Yang Lv
div class="preformatted">Dear all,
what is currently regarded as the optimal strategy to select genes for
machine learning analysis? Taking all of the 40k or so genes is not
doable (at least with randomForest, which I use). "Bioconductor...using nsFilter with argument var.cutoff=0.75,
however I am not sure how that is calculated. Are the genes sorted
according to absolute variance? If yes, is…
updated 14.6 years ago • January Weiner
div class="preformatted">Dear Group,
does limma provide gene set enrichment through a
wilcoxon rank sum test?
I overheard someone discussing that enrichment scores
provided through...rank
sum) are better than GSEA enrichment scores.
I see some old 2005 tutorials usings Dr. Smiths gene
set test.
I am finding difficult to find any vignette that
discuss Gene set test and wilcoxon rank sum.
Ar…
to use the hyperGTest function in the "GOStats" library to
test whether a particular set of E. coli genes has any particular GO
categories over-represented. I am having a little trouble figuring out
how to do this, and would...appreciate advice very much.
I have two vectors containing lists of E. coli genes, "allgenes"
containing all E. coli genes, and "genes" containing a particular
subset
of E…
updated 15.9 years ago • Coghlan, Avril
chooseTopHubInEachModule can be used to identify the top hub gene in each module.
May I know how to obtain the summary of how many genes each gene connected in the same module? For instance...gene A (hub gene) connected with 102 genes, gene B connected with 100 genes, etc. Any script can be used
updated 3.9 years ago • wes
I do DGE analysis with edgeR:
```r
a <- DGEList(counts=counts(dataOffset), group=conds, genes=as.character(rownames(reads[keep,])))
a$offset <- -offst(dataOffset)
a <- estimateDisp(a, design)
fit <- glmQLFit(a,design...TRUE)
```
If we look at the volcano plot from the DGE analysis, there's a weird cluster of genes that are clearly separated from the "volcano":
 for our project. We looked a bit at the data and preprocessed it, but when we wanted to test for differential expressed genes, we got some strange results. Only a couple of genes showed…
updated 8.7 years ago • Lennart.Vermander
calculates the correlation of the GX values (voom on RNAseq counts) of all annotated protein-coding genes vs the query non-coding gene list, then selects clusters based on two thresholds (cluster size - that is, \#coding genes per...a gene set test or GSEA using e.g. the mSigDB gene sets on the coding genes present within each cluster. This would hopefully provide...it, there would be two ways to…
updated 9.7 years ago • m.fletcher
div class="preformatted">Hi BioC user,
I have a problem extracting the gene set I would like to work with.
Here is I work with my data:
normData <- read.delim("normalizedData.txt",sep ="\t")
######### two class unpaired...22929" "10172"
...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:8] "Row" "Gene ID" "Gene Name" "Score(d)" ...
$ genes.lo : chr […
I wish to use DESeq2 to compare the genes in two plant samples at different stages of development- A = early stage (sample A) which will contain genes for leaf, stem...shoot growth but not genes for flower growth and B = later stage (sample B) which will contain genes for leaf, stem, shoot growth and genes for flower...growth. The concept is that this will enable us to identify the genes for flow…
updated 7.2 years ago • pwnoyce
help me with this as I just cant figure it out. I have my DESEQ2 object cts, which includes all my genes. Now I only want to look at 100 genes, which are in the list "risk_genes".
I tried with `cts_new <- cts[cts %in% risk_genes,]` but then...I am left with 0 genes.
What am I doing wrong?
Thank you so much for any help!!
Bine
updated 4.3 years ago • Bine
div class="preformatted">Hi all,
I'm wondering if there is any package that translate the gene symbol
into
its full name.
The result would look something like this page (for the gene name)
http://www.genecards.org/cgi...bin/previous/carddisp.pl?gene=OLIG2
Thanks
--
Regards,
Anh Tran
[[alternative HTML version deleted]]
</div
updated 17.5 years ago • Anh Tran
Hi everyone,
I want to compare expression values of multiple genes in several cancers by using RNA-seq or microarray data. The data is in the form of z-score. I'm using three heatmaps...z-score values are bigger than specific number and median of samples. In each heatmap, rownames are genes and colnames are cancers. What is the best way to present these data in a professional w…
updated 8.9 years ago • sh88.arman
topGO, to perform GO analysis in a RNA-seq data set. I have an small data set of 104 significant genes that I called “sigG”.
Firstly, I used genefilter to find genes that have similar level of expression than my “sigG”. For...each sigGene I got 10 genes which make a background set of 1040 genes (backG).
I run topGO but I found results that make suspect that something is going...wrong.…
updated 8.9 years ago • colaneri
NBt, vars="groups")
s<-get$summary
"s" is a dataframe which contains the significant genes for each comparison, each experimental group vs. the control group.
I got around 6000 genes for each comparison but...Are the results in descendent order of significance? Can I select for example the 30 first rows (genes)? or how many should I select? If they are not in a particular orde…
preformatted">Is there an elegant way to find the chromosome, start and end position
to a given gene symbol via rtracklayer.
In the table browser on USCS website I can provide these information
by
pasting a list of identifiers...My found solution is kind of indirect by first getting a table of all
UCSC names together with gene symbols, finding the corresponding UCSC
names to my symbols and th…
updated 16.5 years ago • Christian Ruckert
div class="preformatted">if i have two lists of differentially regulated genes (they could be
from 2
different statistical tests, or differentially regulated genes in two
treatment
groups) which
updated 22.0 years ago • rkakkar@uchicago.edu
Dear bioconductor community,
is there an R tool that generates a coverage plot around gene bodies like the one created by the [RSeQC][1] tool?
Preferably working on region information stored in GenomicRanges objects
updated 3.9 years ago • svenbioinf
Hello,
I'm looking at the featureCount flag -t and the gtf file for my organism of study, and the gtf file has the following feature options: gene, exon, transcript, and CDS. The manual indicates that exon is the default value for -t, but I have the following questions:
1...t and the gtf file for my organism of study, and the gtf file has the following feature options: gene, exon, transcript…
updated 2.2 years ago • HS
class="preformatted">Hi,
When manually checking p-values from edgeR, I found the p-value of
this
gene difficult to understand. The CPM of this gene in our study is
like
this:
control replicate1: 0
control replicate2: 0
control...replicate3: 34.62
I fitted GLM with model.matrix(~treat1 + treat2 + treat1:treat2). To
find
out genes under significant interaction effect, lrt <- glmLRT(fi…
<div class="preformatted">Dear Pablo,
If you type ?annotatePeakInBatch in a R session after
library(ChIPpeakAnno),
you will notice that you can annotate your peaks with your own
annotation or
built-in annotation dataset.
The following are a few built-in annotation datasets.
data(TSS.human.NCBI36),data(TSS.mouse.NCBIM37), data(GO.rat.RGSC3.4)
and
data(TSS.zebrafish.Zv8). You probably alre…
updated 15.0 years ago • Julie Zhu
I have RNASeq counts for one gene that was treated with 12 different drugs (with 3 replicates each).
I was wondering if anyone could please tell me which...I have RNASeq counts for one gene that was treated with 12 different drugs (with 3 replicates each).
I was wondering if anyone could please tell me which R...package I should use to detect differential gene expression to identify which treatme…
Hey mates,
My script is running perfectly and produces an graph with the genes connected to each other and the pathways. However, now I would like to remove the pathways connection and only have the...genes connected to each other.
Here is a sample functioning code that resembles my script;
```r
install.packages(BiocManager...3836", "4176", "1017", "249")
# Pathway enrichment analysis
enriched…
updated 18 months ago • Antonio
seq experiments and now have coordinates for a list of enhancers. The next question is what genes are potentially regulated by these enhancers. To get a quick idea, we wish to retrieve 5 genes flanking each of these enhancers...and GSEA analyses. Can anyone recommend some package(s) that would be a good start to retrieve the genes? Thanks
updated 10.5 years ago • doublehelixlf
Hi
I am using edgeR for differential gene expression analysis. The following command :
> summary(de <- decideTestsDGE(lrt.CHvsH))
gives me this result,
> summary...de <- decideTestsDGE(lrt.CHvsH))
[,1]
-1 1870
0 9649
1 515
How can the list of genes which are down regulated (1870 genes in this case), up regulated (515) and those which show no c…
updated 10.4 years ago • p_das
Recent ...
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My understanding was …
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