div class="preformatted">Hi
Is there a way to convert non-HUGO gene symbol identifiers to entrez
gene or other ids?
Example:
ACSL1 aka ACS1; LACS; FACL1; FACL2; LACS1; LACS2; ACSL1
Thanks in advance
-burak...alternative HTML version deleted]]
</div
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data for affy oligonucleotide microarray data .
How can I read the data into R ? and how can I identify the
upregulated and
downregulated genes ?
[[alternative HTML version deleted]]
</div
updated 13.3 years ago • Shravanthi P
p-value, should all of them be select for GSEA, or there is a rational way of choosing the number of DEG for GSEA
working with data coming from deep sequencing of 48
small
RNAs libraries and using edgeR to identify DE miRNAs.
I could not figure out how to design my matrix for the following
experimental design:
I have 2 varieties...in 4 physiological stages. None of them
represent a control treatment. I'm particulary interested on
identifying
those miRNAs which modulate their expression dependent on genotype…
updated 13.1 years ago • Danie
I ran DESeq on this subset.
After I ran the two analysis approaches, we have observed that we identify an higher number of DE genes using the DESeqDataSet that includes the 4 conditions (174 DE genes) than when we perform
updated 4.0 years ago • giulia.lopatriello
ID in each table cell, which should be the best one, as they are sorted according to the total number of identified peptides?
OR
2. Is it better to take all protein IDs in each table cell? This way we are accounting for simultaneous
updated 5.8 years ago • harelarik
<div class="preformatted">
Hello all,
I have a question while I am using the limma package to
identify
differentially expressed genes: should I perform gene filtering
after
normalization to exclude genes that are likely unexpressed in the
samples
before fitting the linear model. With my limited stats knowledge, I
believe
the inclusion of 'unexpressed' genes may affe…
updated 16.1 years ago • Peng, Fred
will be a reasonable threshold? I’m sure that for many experienced people doing DGE it should be a number that is sounded as a correct a safe threshold. I will like to have some advice regarding this question.
2. I understand...that DESeq2 perform independent filtering, and that for this purpose it identify a threshold base in counts and remove genes that given the counts cannot produ…
updated 9.7 years ago • colaneri
I am using a dataset that was annotated using Ensembl version 87 of human reference genome version 38. I wrote an R script to access certain values for that data (FASTA sequences...I am using a dataset that was annotated using Ensembl version 87 of human reference genome version 38. I wrote an R script to access certain values for that data (FASTA sequences for the protein-coding genes). However …
div class="preformatted">hi; I am wondering what versions of:
"miranda","mirbase","mirtarget2","pictar","tarbase","targetscan"
are provided by the current version of 'RmiR.Hs.miRNA
updated 12.1 years ago • Hamid Bolouri
Hi,
My workstation is running Debian 10 with the default version 3.5.1 of R. I need to use the Bioconductor package "GoSeq" to perform functional enrichment tests as described in “Running...trinityrnaseq/wiki/Running-GOSeq).
I got a trouble with it. The package "GoSeq" exists only for “R version "3.6" in Bioconductor Release 3.10 which works with R version 3.6.0. After updating the R to the l…
updated 5.9 years ago • gdalsky
div class="preformatted">Hi,
I tried to install the new version 1.4, however, noticed that neither
the default (getBioC() ) nor explicitly calling getBioC("cdna") would
install the vsn
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
updated 9.8 years ago • willmacnair
Hello,
I encountered a rare problem with segment() in the DNAcopy package. Specifically I see artifactual segments with ouptut$loc.start greater than output$end.start and output$num.mark=0 and output$seg.mean=NA.
In my case, it seems to be caused by "chromosomes" (contigs) with empty copy number data point (NAs). Here is a minimal example to try and illustrate the problem:
<pre&…
<div class="preformatted">I am running R 1.5.1 and I have installed the affy package version
1.2.1. When I start R and select library affy I get the following
error.
Any help?
Isaac
P.S. I have installed HDF5 and rhdf5...div class="preformatted">I am running R 1.5.1 and I have installed the affy package version
1.2.1. When I start R and select library affy I get the following
error.
An…
updated 23.3 years ago • Isaac Neuhaus
div class="preformatted">Hello, BioC folks
I wonder whether there is a way to retrieve the total number of human
genes
annotated in Pathway of REACTOAM, one biomaRt mart.
Thanks a lot!
Gilbert
</div
According to the Bioconductor web page for DMRcate, it looks like it is available for Bioconductor version 3.18 but this installation fails:
```r
> BiocManager::install("DMRcate")
Bioconductor version 3.18 (BiocManager 1.30.22...package(s) 'DMRcate'
Warning message:
package 'DMRcate' is not available for Bioconductor version '3.18'
A version of this package for your version of R …
updated 2.0 years ago • Daniel E. Weeks
Dear Bioconductor Maintainers:
I encountered a version conflict when trying to push updates to scQTLtools: Push modifications today but was rejected, so I used "--force" and...received error:
```bash
"Error: Illegal version bump from '1.1.0' to '0.99.14'."
```
but Bioconductor website shows version 0.99.12 (matches my local version before modification...Question**: Why does the remote …
updated 7 months ago • XFWu
command.
BiocManager::install("xcms")
BiocManager::install("MSnbase")
I noticed the version I installed through this command is not the latest release version of these two packages. I am not sure if this is the...developers issue or the *install()* function does not refer to the latest version. For now, I just manually download the tgz file to install the latest version.
Can any…
updated 6.1 years ago • wang.lingjue
Seq data which i mapped and used tophat for mapping splice
junctions,I would like to use EdgeR for identifying differentially
expressed genes.
Do you have an idea if i can use tophat out put file as input for
edgeR?
Best Regards...Asmaa
[[alternative HTML version deleted]]
</div
<div class="preformatted">Hi All
I am trying to use crlmm package for doing the genotyping and CNV
analysis on a set ~200 samples genotyped on Illumina Omni5 array.
I tried following the vignette (seems a bit dated) and got some
errors(see below)
http://www.bioconductor.org/packages/release/bioc/vignettes/crlmm/inst
/doc/IlluminaPreprocessCN.pdf
Also searching a bit more I found multipl…
updated 11.8 years ago • Abhishek Pratap
advice on how best to generate this myself.
Thank you.
Regards, Adai
[[alternative HTML version deleted]]
</div
updated 12.1 years ago • Adaikalavan Ramasamy
pre>
<pre>
Warning in install.packages :
package ‘MacroCAIC’ is not available (for R version 3.1.2)
> install.packages("CAIC")</pre>
<pre>
Warning in install.packages :
package ‘CAIC’ is not available (for R version
updated 9.9 years ago • Gabi
div class="preformatted">Hi,
Can one access builds of old versions of bioc packages?
For example, is it possible to get and install all versions of e.g.
'Rsamtools' that have at any point
Hi,
Trying to install TCGAbiolinks, which has version 1.2.3 of SummarizedExperiments. When I install via biocLite(), I get version 1.0.2. I tried checking out the...there.
I also tried removing the package and reinstalling it, with no improvement.
R version: 3.3.1
Bioconductor Version: 3.2
What am I missing?
Any help would be nice,
Gaius
updated 9.2 years ago • gaiusjaugustus
I have some RNA-seq samples from mouse, 2 conditions with 4 replicates each, read quality is good and for each sample 85-90% of reads align. The number of aligned reads in millions are:
Condition 1 replicate 1: 100
Condition 1 replicate 2: 79
Condition 1 replicate 3: 52
Condition...with 4 replicates each, read quality is good and for each sample 85-90% of reads align. The number of alig…
updated 8.1 years ago • Mike
like to use the qAlign function in QuasR. However, I do not see any parameters for specifying the number of mismatches allowed (-v parameter in bowtie) or the number of alignments (-k parameter in bowtie) to output for a multi
updated 6.0 years ago • Julie Zhu
<div class="preformatted">Hi Al,
The current version of lumiHumanAll.db was built based on Illumina
Company
provided annotation files. As the probes were designed based...div class="preformatted">Hi Al,
The current version of lumiHumanAll.db was built based on Illumina
Company
provided annotation files. As the probes were designed...Human WG6 chips, and lumiHumanAll.db.
After
> …
updated 17.5 years ago • Pan Du
I asked my question to Affymetrix support and they answered:
This difference can be due to a number of reasons.
Firstly, the CDF file is the array layout information designed for 3'
IVT array analysis, and are therefore...Thank you,
Sophie LAMARRE
Biostatistician - Toulouse (FRANCE)
-- output of sessionInfo():
R version 2.13.0 (2011-04-13)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[…
updated 14.0 years ago • Guest User
BiocManager")
>
> BiocManager::install("illuminaHumanv4.db")
Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in
vignette
updated 2.2 years ago • Aytaç
need to extract biologically relevant results at single patient level. For context, we have a big number of brain tumours but due to the delicate structure of the brain and funding, we do not have the capacity for biological...the expression of multiple brain tumours with a certain classification to that of normal tissue and identifying significant results.
However, in the process of making in…
updated 2.0 years ago • Manthos
But I get the following error:
```{r}
Error in `[.default`(tab, , 1) : incorrect number of dimensions
```
I'm not sure if this is a bug or I am doing something wrong. I would be most grateful if you could shed some
Enter the body of text here
I did RNAseq of a Drosophila cell line. By using RNASTAR in Galaxy I am getting high number of reads mapped to too many loci.
(uniquely mapped 60 %, mapped to multiple loci 10 %, mapped to too many loci 24 %).
Later when I...text here
I did RNAseq of a Drosophila cell line. By using RNASTAR in Galaxy I am getting high number of reads mapped to too many loci.…
updated 3.7 years ago • vasa.broz
I use a cell line, in which, as all in vitro cell-based experiments, the passage number will affect the gene expression (the influence of the passage number is well-known and accepted in literature).
I have...N=2 (which N=the biological replica that corresponds to passage number). Each N has 1) control, 2) substance A, 3) substance B, and 4) substance C (total number of samples=8, 4 for each pa…
updated 3.2 years ago • swn281
the main error is around annotation:
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.12 (BiocInstaller 1.10.0), ?biocLite for help
> biocLite("hthgu133pluspm.db")
BioC_mirror: http://bioconductor.org...Using Bioconductor version 2.12 (BiocInstaller 1.10.0), R version
3.0.0.
Installing package(s) 'hthgu133pluspm.db'
Warning message:
package ???hthgu133pluspm.db.…
We have a project running in version 3.4.4 of R. When we build it, we are getting an error that BiocInstaller is not available (see below).
According to https...on what could be causing this or what we could try differently? We'd like to avoid upgrading our version of R if possible.
Code should be placed in three backticks as shown below
```r
> source("https://bioconductor.or…
updated 3.4 years ago • Kevin
I am attempting to extract copy number from EPIC and EPICv2 arrays.
I have tried some things but run into the same issues as reported [here](https://support.bioconductor.org
updated 9 months ago • Adam
Hello,
I would like to use coseq to cluster my results based upon transcripts that were identified as differentially expressed by DESeq2. Coseq mentions that I can take the object (e.g. dds) and use that directly...must be one of
the following: none, TC, DESeq, TMM, or a vector oflength equal to the number of columns
in ‘y’
```
Looking at the code, I did specify a valid option …
I am trying to benchmark methods for detecting cell outliers. Although it is not very meaningful to identify a very small number of outliers in scRNA-seq datasets that usually contain thousands of cells, it may be a straightforward
updated 7.6 years ago • luke.zappia
two scRNA-seq datasets, both derived from a heterogeneous population of cells (comprising similar numbers of cell types and subpopulations). One sample has been treated with a drug, the other has not. While I can separate out...the cellular subpopulations in each dataset, what I want is to then identify differentially expressed genes that result from the drug treatment - in each of the individual…
updated 8.1 years ago • d.depledge
Hi,
I changed to R version 3.2.0 and DiffBind version 1.14.3. The problems are:
- The heatmap produced by
data = dba(sampleSheet="HistoneData\_C.csv...minOverlap=2)
plot(data)
is different that in previous version that I had (1.8.5) (grouping of samples is different). Is this because of a change in the method or a bug? I tried several...versions of parameters.
- The side colours in heatma…
updated 10.5 years ago • pkra
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updated 2.6 years ago • yakes61237
div class="preformatted">Hello
I am tryng to install GenomeRanges in R, svn last version, but the
required version of IRanges is not available (1.13.23). Details are
below.
Thank you in advance
> biocLite("GenomicRanges...BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.3.7.
Installing package(s) 'GenomicRanges'
Installing package(s) into '/stockage/…
updated 13.8 years ago • Duhaime Johanne
and hope to
seek suggestions on completing the analysis within 1 to 2 months. The
objective is to identify differentially expressed genes, and to
perform gene ontology analysis. Now I am at a loss given the diverse
packages...from.
_________________________________________________________________
[[alternative HTML version deleted]]
</div
updated 17.1 years ago • Daren Tan
preformatted">It looks like there may be more than a 3UTR sequence for the same
transcript that we identify through three keywords: hgnc_symbol,
ensembl_gene_id, ensembl_transcript_id.
It maybe caused by a bug in my script...such a weird situation real ?
Thank you,
Maura
tutti i telefonini TIM!
[[alternative HTML version deleted]]
</div
updated 15.5 years ago • mauede@alice.it
Hi all,
I am trying to identify genes that are specific to a cell type of interest by comparison with a large number of other cell types. To this end
updated 7.8 years ago • john.ouyang
Hi, guys!
I was trying to install DESeq of Bioconductor 3.12 in Ubuntu under R4.0.4, but it didn't work. Moreover, I was told that package 'DESeq'is not available for this version of R. But what I'm confused is that I can install DESeq2 or other package of Bioconductor 3.12 successfully and I can't install DESeq under R4.0.3, either.
Is any idea here? I really need your help.Thanks!
```r
…
updated 4.7 years ago • Evy_00
biocLite.R", R calls
for "http://bioconductor.org/biocLite.R" which explicitely checks for
the R version and returns an error (R version should be above
R.2.1.0).
When taking a look at the biocLite.R script, this line caught...my eye:
## R versions less than 2.1.0 need to use the old (BioC 1.5) version
of
getBioC.R
but I have no idea where to get the old version of getBioC.R
Sorry if this is a simple question for some, I am flying blind on my first attempt at RNA seq with a demand for immediate deadlines.
I've used a process of Salmon (with FASTQC) -> tximport -> DESeq2 and I've thrown in a bit of Scater for some PCA calculations. however, I would like to plot the absolute number and percent of mapped reads to each experimental sample (6 controls, 6 …
<div class="preformatted">Dear Bioconductor Subscriber,
Just so you know that we released Custom CDF version 14 at
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF
_download.asp#v14 Our brainarray BioC repository is updated too.
In this version, tiling chips are discontinued because of low
usage, JCVIG and JCVIT cdf type is added for Medicago chip, an…
Recent ...
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