three replicates.
I have already analyzed these data using limma, just to have an idea
of
regulated genes at 6 hr and 24 hr, but now I would like to cluster the
data
across the time points to group the genes according to their
expression...profile.
My question is: what method should I use in order to do this? I have
checked
already the timecourse<http: bi="" html="" oc="" packages...package,…
Order by: Relevance
On 10/09/2011 11:00, bioconductor-request at r-project.org wrote:
> Subject:
> Re: [BioC] Clustering of 30,000+ genes
> From:
> Sean Davis <sdavis2 at="" mail.nih.gov="">
> Date:
> 09/09/2011 11:08
>
> To:
> January Weiner...gt; I'm struggling with co-expression analysis, and for that I would
like
>> > to …
updated 12.6 years ago • Thorsten Forster
packages in an HPC environment, using OpenMPI and R's `doMPI` package on my university's ~3000 node cluster. Mostly my workload parallelises trivially, but `opls` from the `ropls` package is slow.
Please forgive me for being naïve...but what's the best way to profile it? Running it locally I just get "(sources are not available)" in RStudio (with `profvis`) and although I can wget the tarball…
updated 2.5 years ago • Jack
of low RINs (2-4) in a bunch of them compared to the others, I am getting very widely varying mapping rates (15%-70%) and therefore counts per sample (e.g. 8,000,000 mapped reads vs 40,000,000). Plus I can't really use RIN/mapping...there a preferred way of analyzing this type of data? If I do the usual VST through DESEQ2 I get a cluster of samples with irregular high expression of a lot of genes…
updated 5.2 years ago • chris86
a set of differentially
expressed probes, let's say that we want to perform a hierarchical
clustering to "visualize" the differential gene expression profiling
adding a third class to evaluate the similarities...CLUSTER?
In my opinion the implicit constrain of this approach is to introduce
a "literature-bias" , because the replicated genes...for example p53, ER and so on). In this way we force
i…
annotation files. As the probes were designed based on
different
sources, lots of probes have no EntrezID available. One option is to
blast
the probe sequence against the latest human genome to get the
mappings. The
probe...lumi package. You can also check
https://prod.bioinformatics.northwestern.edu/nuID/
, which list the mapping between nuID and corresponding annotations. I
am
trying to convert…
updated 15.9 years ago • Pan Du
org.Hs.egALIAS2EG)<br/>
$ALPK3<br/>
[1] "57538"</code>
As far as I can tell, "MAK" is correctly mapped to the gene ID 4177 and incorrectly mapped to the gene id 57538 (the latter is the id corresponding to gene symbol
updated 7.8 years ago • af2202
I have a gene co-expression network obtained from RNA-seq data which has more than 10000 nodes and more than 10lakh edges. I need to...cluster this network. Can anyone please suggest a method to cluster this effectively.
I tried with igraph R package, in igraph...package many clustering methods are there. How can I identify which is the appropriate method for large gene co-expression network
updated 5.1 years ago • aiswaryabioinfo
div class="preformatted">Dear List,
I am exploring several methods of clustering gene expression
microarray
data, and I have some problems with the k-means method. Is scaling
necessary for my data...types. The data ranges from
2.5e+00 to 1.9e+05, and has a median of 2.8e+02. The strategy in this
clustering is to increase k, until no new expression relationships
among the 5 cell types are foun…
updated 14.4 years ago • Edwin Groot
<div class="preformatted">Hi all,
I am working on a single color expression 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 the normalized data (MA),
to
retrieve the distribution across the samples.
But I am wond…
div class="preformatted">Hi all,
Suppose I have 2 matrices A and B (they are gene expression profiles).
And I want to measure how good each of this matrix is.
So I intend to compare A and B with another "gold
updated 15.9 years ago • Gundala Viswanath
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 12.2 years ago • wang peter
gt; As section 5.3 of the vignette explains, the transformed data can be
used for applications like clustering of samples. I was considering
the best way to use it instead for clustering genes of a time-series
experiment. I would...have to account for gene length to make different
genes comparable. This could be done after the transformation, by
dividing by appropriate constants...Both DESeq2 tra…
updated 10.0 years ago • Michael Love
Dear all,
after clustering a gene expression dataset, please can you advise, how can i extract the group of gene names corresponding to 
updated 7.1 years ago • Bogdan
that is essential. But, in that organism only three are
known.
If I have the expression for all genes, is it possible to cluster
all expression in relation to expression of this three genes?
I am looking if any of that genes...group together this three. I can
do a cluster with all genes, but I would like to cluster one group
knowing that another group exist.
What you mean about my …
edgeR and voom-limma. My goal was to evaluate each methods on my data. Now I would like to perform clustering with the genes found differentially expressed (DEG) by each method to see how well these genes discriminat my two...have to shoot my counts through some type of variance stabilizing transformation
Should I do all my clusterings with rlog data and the 3 sets of DEG ?
I wonder if it is re…
updated 8.0 years ago • User34591
Hello, just a quick question today. I am an undergraduate using cluster profiler for functional analysis of gene sets. The graphs being made by enrichGO and GSEA put out a variable called...We think it is some transformation of our variable "set_size", which is count numbers of the gene sets, but it appears as though there is some sort of transformation put on it that I can find no info on. Thanks
updated 11 weeks ago • Matthew
div class="preformatted">Hi there,
Which packages and functions are commonly used for mapping mouse genes
to
homologous human genes ?
Thanks,
Zhihao
[[alternative HTML version deleted]]
</div
updated 13.5 years ago • Zhihao Ding
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...which I use preferentially (mostly
because it gives me a p-value surrogate), indicates two main clusters
with AU p-values of 99 and 98, and BP p-values of 0 and 1,
re…
pathview. I normalised an expression dataset, to the point where i only have to columns (one is the gene\_id, and one the fold change).
My file looks like this:
<table border="0" cellpadding="0" cellspacing="0" style="width:183px">
<tbody...keys.align = "y", kegg.native = TRUE, key.pos = "topright")</pre>
The result however is that no genes are mapped. i get this message
Note: …
div class="preformatted">Hi All:
I am clustering ~500 genes using hclust of R. Visualizing cluster
membership in the dendrogram becomes impossible with so many...genes in
each
cluster. with all the labels overlapping..Is there a way of printing
the
dendrogram on multiple pages so that I...can clearly see what is in each
cluster? Or is there a way of splitting the tree so that I see what is
i…
updated 20.6 years ago • Subramanian Karthikeyan
c('time_id', '0', '3')<br/>
c(0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 1)</code>
Looking for the genes with maximal fold changes in the size factor-normalized counts identifies a large number of very similar genes (i.e...names identical apart from a number, no difference in description on GeneCards) with log2 fold changes less than -4. However these genes are highly variable, and.…
updated 8.2 years ago • willmacnair
Hello everybody!
I have a question about an analysis of my polysome profiling experiment.
In my case I have to conditions (with and without treatment) and two sample types for each condition...Hello everybody!
I have a question about an analysis of my polysome profiling experiment.
In my case I have to conditions (with and without treatment) and two sample types for each condition, the mRNA…
m analyzing some single cell data using Single Cell Experiment package.
I'm trying to detect marker genes between clusters using the **findMarkers()** function.
In particular, I wanted to check how many marker genes there are between...cluster 3 and 7, which have *FDR* < 0.01 and a *LogFC* |1.5|.
When I construct a marker set for cluster 3, the amount of genes with a FDR...lt; 0.01 …
updated 4.6 years ago • ludmi.b
In the [RNA-seq workflow: gene-level exploratory analysis and differential expression](http://master.bioconductor.org/packages/release/workflows...experiments) **9 Time course experiments**
There is a sentence saying
> We can furthermore cluster significant genes by their profiles. We extract a matrix of the shrunken log2 fold changes using the coef function...DESeqDataSet(fission, ~ s…
updated 3.9 years ago • shangguandong1996
div class="preformatted">Hi!
I was mapping probeIDs from 133plus2 arrays to entrezIDs using
aafLocusLink, some months ago with an earlier version of the package...and now with the current annaffy and hgu133plus2 packages. I compared
my results and some probes no longer got mapped with the new package
version, e.g POU5F1. The gene does have probes on the array, all just
happen to be x_at...pro…
updated 14.4 years ago • Merja Heinaniemi
Hi.
We are trying to investigate the mutational clusters in various TCGA cancers, and I am wondering which R package you suggest to count them.
In fact, we want to measure the...no. of defined mutations, like C>T, within specified genomic distances.
I would appreciate your kind help
updated 8.3 years ago • niavarani
<div class="preformatted">Hi,
At first I'd like to explain that my RNAseq experiments involve RNAi
depletions of RNA decay factors, so one should expect to see more
upregulations. The libraries are ribodepleted, paired end and
stranded. After
mapping with tophat I use HTSeq/DESeq combo to discover DE genes
(among
tophat genes.gtf)
Using raw counts I run DESeq on default settings and I get…
updated 11.6 years ago • Michal Lulu
on my todo list
for far too long.
Can you please elaborate (or point me to a doc) on your probe mapping
process? transcript to gene redundancy is the big issue here, which
CTNND1 suffers from.
What are your thoughts on a...from the Illumina manifest file. Rather we have taken the
> probe sequences and done a re-mapping to the genome and
transcriptome.
> The RefSeq IDs that we assi…
updated 12.6 years ago • Mark Cowley
I have analysed my data (from the Epic Illumina array), using limma to find single differentially methylated CpGs (DMPs), and DMRcate to find DMRs.
The data and the model is exactly the same for both analyses; using no intercept and specifying a contrast of interest.
When I compare the lists of genes that the significant DMRs and DMPs map to, there is of course an overlap, but more than half…
updated 4.7 years ago • anne-kristin.stavrum
div class="preformatted">
Hi,
I'm trying to make nice comparison of GO profiles for three samples.
How can do this with goProfiles, I already have GO terms and I can
easily do the profiles using entrez
updated 11.6 years ago • Guest User
<div class="preformatted">Hi,
I am doing some mapping of affymetrix probeset IDs to gene symbols
using
package hgu133plus2.db.
As the following example illustrates, each of the 40686 mapped
probesets
maps to exactly one gene symbol.
> library("hgu133plus2.db")
> x <- hgu133plus2SYMBOL
> Llength(x)
[1] 54675
> count.mappedkeys(x)
[1] 40686
> …
updated 13.6 years ago • Christian Ruckert
div class="preformatted">Hello.
I have a problem trying to get a mapping between differents Gene IDs
and GO Ids.
I have found function to get mappings between LocusLink Id and Unigene
and...GO ids.
But now, I need mappings between GeneBank and GO ids, and GeneNames
and GO ids.
Anybody know functions to do so ?
Thanks for any help.
____________________________________________________________
Is there a simple way to map a list of probe sequences to a genome ? The use case is probes of a custom-designed NanoString assay. The RLF file provided by NanoString has a gene symbol and probe sequence, but not the genomic coordinates of the probe. I don't want the hassle of running `` bowtie `` for a small...use case is probes of a custom-designed NanoString assay. The RLF file provided by Nan…
updated 7.0 years ago • Dario Strbenac
to do GO enrichment analysis. I work on Cannabis sativa, which is a non-model organism. There are no GO terms for Cannabis, so I cannot make use of the orgdb or biomart functions in R. However, I have generated a file with GO terms...mapped to protein id from the original fasta. My file looks like this:
```r
!db db_object_id db_object_symbol qualifier term_access…
updated 23 months ago • Lucía
Hi,
I'm trying to cluster rows and columns in DESeq2 and show it in a heatmap. I've tried this:
heatmap.2(assay(vst)\[select,\], col = hmcol,
 ...trace="none", margin=c(8, 8))
I think my problem is revealed when the scale = 'row', the genes don't seem clustered, yet when scale='none' I see high medium and lowly expressed genes in separate clusters. …
div class="preformatted">Dear List:
Happy New Year!
I have a question regarding mapping the gene to a copy number
variations.
I have affy 250 nsp mapping arrays results. Now I try to map the
result for each probe...to a gene.
then, I can perform correlation analysis between the copy number
variation and gene expression level for candidate...nbsp;genes.
I think I have an idea to ma…
updated 12.3 years ago • Xiaokuan Wei
to M values. MDS plots are created using beta and M values.
I find that beta values and M values cluster differently. Beta values do not show clustering by sex but M values show clustering by sex. I find it hard to figure out...how going from beta to m-values can change the clustering profile. Is this normal or is something wrong somewhere? There is also this weird stripy clustering going on …
updated 5.1 years ago • rmf
Hello,
I finally ran maSigPro and Would like to save final results of DE genes in data.frame format. I also would like to extract the genes that are in the same cluster. how can I do that ?
Thanks in advance
updated 7.2 years ago • simonjean434
most
recent release version) for the last couple of days, and noticed that
some of our usual marker genes appear to not be present in the
annotation package. These genes are present in current and previous
versions of the Affymetrix...probe -> gene mappings from NETAFFX.
For example, transcript cluster 16966809 should correspond to gene
symbol PDGFRA and Entrez...hugene20sttranscriptcluste…
updated 9.9 years ago • Cornwell, Adam
Dear all,
Using an RNASeq experiment of 16 samples, I would like to cluster genes, and not samples. My aim is to identify subsets of genes that behave similarly across the samples, which could...Dear all,
Using an RNASeq experiment of 16 samples, I would like to cluster genes, and not samples. My aim is to identify subsets of genes that behave similarly across the samples, which could be possib…
updated 6.5 years ago • Jane Merlevede
When I was doing GO and KEGG enrichment, some weird things happened. I used all the differential genes to do the enrichment, only 6.99% of input gene IDS are fail to map. But when I separated the upregulated genes and downregulated...genes from all, and did the enrichment separately, 8.03% of input gene IDS are fail to map for downregulated genes, 8.09% of input...gene IDS are fail to map for upr…
updated 2.3 years ago • waltsonwang88
Hi
I was doing a gene ontology analysis on a set of differentially expressed genes. The goana function returns an error saying ," No genes found...for differential expression analysis ('countdata' represents the dataframe containing counts of each gene in each of the samples) :
<pre>
> gns <- select(org.Hs.eg.db, row.names(countdata), c("ENTREZID","SYMBOL"),"ENSEMBL")
'sel…
updated 6.5 years ago • fawazfebin
div class="preformatted">Hi all,
I have a normalized microarray (Affy) gene expression data for
different
time points and i would like to cluster genes with similar expression
pattern ,which package
updated 12.9 years ago • Asma rabe
Below, GG is the list of gene symbols to be mapped into entrez.
The code is:
geneMapping2= select(org.Hs.eg.db, GG, c("ENTREZID","GENENAME"),"ALIAS")
The error...Below, GG is the list of gene symbols to be mapped into entrez.
The code is:
geneMapping2= select(org.Hs.eg.db, GG, c("ENTREZID","GENENAME"),"ALIAS")
The error is:
Error in .testForValidKeys(x, keys, keyt…
updated 4.2 years ago • omarrafiqued
Hello everyone,
I am using the Bioconducter package [TCseq][1] to cluster genes given the gene expression matrix. I have used this package before when I had raw count data and it worked really...steps provided in the manual of the package. Here is my concern how can I create tca object using gene expression matrix after normalization.
Thanks,
[1]: https://bioconductor.org/packa…
updated 4.8 years ago • bioyas
PolII_narrow_peak, upstream = 3000, downstream = 3000, conf = 0.95,
by = "gene", type = "start_site", TxDb = txdb,
facet = "row")
```
Secondly, the main issue I'm running into is when I attempt to plot the gene body profile...nbin = 800,
type = "body",
by = "gene",
weightCol = "V5",…
updated 2.5 years ago • william.ho
about the library size you mentioned.
> Is it the total reads of a sample or the sum of the reads mapped to
each gene.
> I mean, if the total reads of a sample is 1,000,100,
> but when I mapped the reads to the gene, I got a list of gene...with
reads mapped to it, and the sum of this is 900,000.
> Do I use 1,000,000 or 900,000??
[[alternative HTML version dele…
updated 12.0 years ago • Sooby
the raw CEL files I select the top 200
with the highest variance before using this data for clustering.
Below is the code I am using. Could anyone tell me where I might be
going
wrong - i.e. why my
cluster files (e.g. OvarianFzy.cdt...gradient ?
I apologize in advance if my question is not clear,
I am only a beginner at using the clustering methods.
Thank you,
Mark
# Take the 200 genes with h…
updated 12.3 years ago • Mark Baumeister
preformatted">Hi,
Is it possible to obtain a quality metric indicating the "tightness"
of
each cluster generated by the hopach package? - e.g the silhouette
averaged across all cluster elements; or the distance averaged...over
all
pairs of cluster elements. makeTree appears to calculate an average
distance for each node in the dendrogram (these values are displayed...by
the MapleTree viewer),…
div class="preformatted">
I have a RMA normalized genes expression datset with 22810 rows and 9
columns( types of promoters) and a subset of the data is as follows:
ID_REF GSM362180...5.242403911 5.060605782 5.458148567 5.890061836
-- output of sessionInfo():
I want to do a clustering of the above and tried the hierarchical
clustering:
d <- dist(as.matrix(deg), method = "eu…
updated 11.5 years ago • Guest User
I downloaded the human Ensdb AH75011 and the Txdb AH75758.
When I call the "exonsBy(object , 'gene')" method on the Txdb object it automatically converts the ENSG to GeneID.
It seems that around 20% of my ENSG ids cannot be...not present in my Txdb object after having applied the exonsBy method (even if in Genecards it is mapped to EntrezGene 4537 ).
Am I missing something ?
Thx a lot
updated 4.4 years ago • atariw
to a cluster, but seems to force to put all genes to their cluster, not allowing a semi-supervised clustering. Could we impose...force to have a cluster with certain genes and "freely" cluster others?
Can other information than the expression, like GO, pathways, be used...to build the clusters? AFAIK one can use a parameter, like time, treatment or alike to build the clusters,…
updated 8.0 years ago • Lluís Revilla Sancho
I'm a college student and use sc3 for my graduation thesis. I have got 3 clusters and the expression matrix. I want so show certain gene\`s expression in heatmap besides marker genes and...DE genes. How can I do it？Thanks
updated 5.9 years ago • qq1493438060
from different body parts; oral and aboral parts of small, medium and large sized specimens. We have mapped the reads using tophat2 and run cuffdiff and DESeq2 (with HTSeq count). Using the `` csDendro `` function in cummeRbund the...samples cluster largely by oral/aboral parts, but clustering a distance matrix of rlog-values from DESeq2 the samples group mainly...rlog-transformed raw c…
updated 8.3 years ago • Jon Bråte
imagine the following situation:
For two sample sets (set1, set2) the most differentially expressed
genes are
identified by limma. The p.value correction would be "holm".
Afterwards a
heatmap is printed for these genes. The procedure...gt;= 1
> ## print a heatmap for eSet[selected,]
What can lead to a misclassification in the clustering, say one
sample of
set1 is clustered together wit…
updated 17.5 years ago • Benjamin Otto
hybridizations on every time-point using dual-channel microarrays.
Now we want to detect groups of genes affected by the same TFs using a
gene
clustering approach based on the set of differentially expressed
genes.
Is it generally...appropriate to perform gene expression
standardization
(e.g. by rescaling and recentering) on logged fold changes using such
an
experimental design...correlation, …
updated 16.7 years ago • Serge Eifes
merging the samples of the two experiments into one study, my samples cluster by library type with both rlog and vsd transformations.
It is not surprising since a lot of genes should have an expression...experiment.
I started to check the number of lowly expressed genes in both experiments. It seems that there is no less expressed genes in the experiment with polyA than in the experiment...wi…
updated 8.1 years ago • Jane Merlevede
I keep getting segfaults using `swappedDrops()` on our linux cluster: caught segfault, cause 'memory not mapped'. It works fine on my MacBook, but we cannot find an explanation or solution...on the cluster. I have not had any problems with other functions of the package. I tried a bunch of R versions and packages of `DropletUtils...test_2), get.swapped = TRUE)
*** caught segfault ***
address …
updated 2.9 years ago • wesselyf
normalization of our data.
2) If we perform some sort of clustering of RNA-Seq data, and then
obtain a gene
list from a cluster (e.g. all genes in a cluster) and then want to
perform gene...set enrichment analysis on this gene list, is just using the Fisher's
Exact Test
by itself ok or do we need to account for gene length (e.g. use
GOSeq)? I know
that RNA...Seq data has the bias that longer ge…
updated 12.0 years ago • Julie Leonard
Recent ...
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Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data
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Leo Lahti
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1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
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pl23
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Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
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Michael Love
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For help with interpretation and design of analysis, I recommend working with a local statistician.
Due to time restrictions, I can only…
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Hi Michael,
Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
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