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updated 22.5 years ago • madman@jimmy.harvard.edu
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updated 21.7 years ago • madman@jimmy.harvard.edu
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updated 22.8 years ago • madman@jimmy.harvard.edu
div class="preformatted">This is an automated message sent out weekly to report recent changes
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if I type a function name in R, it'll print the function
for me. Unfortunately, it does so without comments. Is there a way to
get the function with comments?
A related question: how can I access the documentation/comments for
div class="preformatted">This is an automated message sent out weekly to report recent changes
to Bioconductor packages. Please see the files madman/Rpacks/NEWS
and NEWS.old at any time for up to date information...Also, please remember to edit the NEWS file yourself after making any
noteworthy changes to the packages - follow the format used in these
files and make sure to sign your name to …
want to run an idea past this list as a sanity check. I would
especially value Gordon and Charity's comments if they have time.
The voom log transformation is essentially:
log2( (count+0.5) / library.size )
It then does some clever...weighting low counts, I'm trying to get rid of the
extra variation from low counts by artificially left censoring the
data.
- I'm using the mean of the libaray…
Is there a way to retrieve history for specific packages? For example, even basic information such as when which version was released
updated 10.5 years ago • igor
to 1.0.3 in the release version of
Biconductor (2.5). This fixes a broken build caused by the recent
update of DBI on CRAN.
BUG FIXES
o The recently release of DBI version 0.2-5 on CRAN fixed a name
mangling bug
whereby a...column name of "end" would silently be changed to
"end__1". This columnname was used internally in Genominator so a
change was warranted. Genominator now depends...…
updated 16.0 years ago • Kasper Daniel Hansen
div class="preformatted">Dear list:
On the Windows version one can bring back R command history at the
prompt
by using a up-ward arrow key. Unfortunately I can not do the same
thing on
a Sun unix machine. I am wondering...if one can set up the history
function
or command editing function, what ever you call that, with the unix
version
of R?
Thanks in advance!
Jianping
updated 19.6 years ago • Jianping Jin
Hi Matt and Nadia,
For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my custom gene sets this way:
goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repcnt = 100000)
After recent update to version 1.18.0, the pipeline crashed and return…
updated 10.9 years ago • Oleg Moskvin
the changes in expression not explained by the cell counts (either because they come from cell types not included in the model...or because they come from free RNA in plasma). We also want to explain the changes in expression associated with each blood cell.
### Data
- Expression values before and after the race extracted from...and platelets).
- Some possible confounding variables (age,…
updated 5.7 years ago • p.figuerola.9
Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file:
##contig=
<id=hla-drb1*15:03...Is there a simple way to get comments from a VCF header of a VCF object? For example, consider the following excerpt of a VCF file:
##contig=
<id=hla-drb1*15:03:01...positives with a list of failed filters and true…
updated 5.5 years ago • Dario Strbenac
div class="preformatted">What follows is some random comments on the use of GRanges for storing
data in the elementMetadata slot. My use case is a lot of very small
ranges (>10M...but very important to me :). I am particular interested in fast
subsetting like subsetByOverlaps.
Comments:
* I find column subsetting on the elementMetadata to be really slow,
slower than it need to be I …
updated 15.3 years ago • Kasper Daniel Hansen
to run an idea past this list as a sanity check. I would
> especially value Gordon and Charity's comments if they have time.
>
> The voom log transformation is essentially:
>
> log2( (count+0.5) / library.size )
>
> It then...low counts, I'm trying to get rid of the
> extra variation from low counts by artificially left censoring the
&g…
automatically test BioConductor packages. As a package developer, how can I upload the experimental source version of a package to get test results from a specific test server?
**Use case:** Our package contains an error that started...to appear only recently and only on Windows systems. The *tokay1* server of checkResults documented the error in our latest BioConductor...version. I would like…
updated 5.2 years ago • p.stahlhofen
div class="preformatted">Hi Lana,
The MSigDB is a good source!
We are planning to have a summer student working on a similar project,
but
using a different database. Maybe we can coordinate...Mon, 12 Mar 2007 14:39:54 -0700
From: "Lana Schaffer" <schaffer@scripps.edu>
Subject: Re: [BioC] Category
To: <bioconductor at="" stat.math.ethz.ch="">
Message-ID: <016001c764ee$f92bf…
treatments, with three replicate individuals each. The species fall into three physiological categories. I would like to identify genes whose response to the treatments varies by physiological category.
I think...as independent (I get apparently sensible results given prior knowledge) but we know from a long history of work in comparative methods that they are not, and I am concerned t…
updated 8.5 years ago • noah.reid
div class="preformatted">Hi all,
I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key
Contributor to Neurological Disease,
Activates and Represses...Figure S1 which basically plots cellular component, biological
process, and
molecular function categories
that differ significantly based on on genes that are differentially
expressed in two conditions. I wonder whether
updated 17.6 years ago • affy snp
<div class="preformatted">Dear list,
I have a theoretical question regarding Filtering on Variation in the
Category package. I've performed an analysis that closely resembles
the
Vignette, but I am still a bit uncertain about the filtering.
In the Vignette the following code is used:
lowQ<-rowQ(eset,floor(0.25*NumArrays))
upQ<-rowQ(eset,ceiling(0.75*NumArrays))
iqrs<-u…
updated 18.4 years ago • Boel Brynedal
groups in my data. The metadata are TCGA-LGG samples and I am interested in phenotype of seizure history. The two groups I am interested in are 177 samples in no seizure history group and 298 samples in yes seizure history...each individual. For example, if I have a gene set 'calcium signaling pathway' enriched in seizure history yes group, I would like to take one individual from the group, calc…
everybody,
I was wondering whether there is a package to cluster a list of genes
to
different GO categories
my problem is as such:
i have a list of genes (a tab delimited file):
id flybasename_gene flybase_gene_id entrezgene...FBgn0034454 37248 protein binding
I would like to try and group the genes in various GO categories,
which are
mentioned here in the last columns. The GO c…
updated 15.0 years ago • Assa Yeroslaviz
I'm troubled because what looks like the same
object behaves very differently depending on my "history."
With a clean history (.Rhistory and .Rdata deleted), I get this:
> library("genefilter")
> data(sample.ExpressionSet)
>...others like it) work:
> varLabels(eset)
[1] "sex" "type" "score"
But if I now quit and save history, then start again and go:
>…
updated 18.2 years ago • Thomas Elliott
I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy...I can't change the y-axis' category order of dotplot result, I don't know the default order of it. I've used ordrBy="x",orderBy="Count",orderBy="geneRatio" in dotplot() parameters, but nothing changed.
Thank you very much!
```
#ego <- enric…
updated 4.2 years ago • Yang
it loads properly. I get the following error output,
however, when I try to run hyperGTest, package Category, on a vector
of Entrez Gene IDs and a vector of the gene universe of the chip. I
suspect I did something wrong when building...0.05, conditional
= TRUE, testDirection = "over")
> params
A GOHyperGParams instance
category: GO
annotation: ragene10stv1
> hyperGTest(params)
Err…
updated 17.2 years ago • Mark W Kimpel
Hi all,
I have a good amount of experience in doing differential gene expression analysis in two categories like healthy samples and disease patients. Now I have three categories of patients at baseline, then at week 16...and week 52. I am thinking to try one way anova on this data. Any information on links or any good sources of DE analysis with anova awould be really appreciated.&…
updated 8.5 years ago • pbachali
the licensing policy of Bioconductor. According to <http://www.bioconductor.org/about/>, the open source policy is:
* __Open source__. The Bioconductor project has a commitment to full open source discipline, with distribution...via a public subversion (version control) server. All contributions exist under an open source license such as Artistic 2.0, GPL2, or BSD. There are many differe…
Dear all,
I have some gene expression data sets. In some of the data sets, I am comparing two age categories, and in some I am comparing multiple age categories. For each dataset, I want to do a two-tailed F test between the age...correctly.
If someone had the time to glance at the code below and edit the line that I should change, so that the code reads: I input the pData (different age catego…
updated 9.1 years ago • StephK
expression (lmFit and eBayes).
I get a high number of DE genes. Most of these belong to Category:
Main. However, some of them, belongs to other categories such as
normgene->intron, control->affx, normgene->exon...As I understand it, empirical Bayes takes into consideration the full
data set. Removing all other categories, some of them which are not
supposed to be changed bet…
Hi,
I'm trying to use the `gate_mindensity2` from the openCyto package to gate out debris from my .fcs files. I'm using https://flowrepository.org/id/FR-FCM-ZZ36 as an example.
I can gate out the debris at the lower end (i.e. left hand side of the gate) but if I want to apply a gate to remove the events on the right hand side, I am unable to do so, even if I set the `positive` argument to TR…
updated 6.9 years ago • biomiha
<div class="preformatted">Dear Bioconductor List,
I have just installed R version 2.15.2 on a Mac
running under Mac OS X 10.7.5. I want to install the
development version of Bioconductor so that I can
access and install the development version of easyRNASeq.
Here is my session record:
version 2.15.2 (2012-10-26) -- "Trick or Treat"
Copyright (C) 2012 The R Foundation for Statisti…
updated 13.1 years ago • Richard Friedman
I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than...the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, I am not trying to do...a ranking approach like GSEA. I would simply like to take advantage of the extensive list of categories in MSigD…
updated 7.3 years ago • Mthabisi Moyo
div class="preformatted">Hi,
I am having troubles with cateGOry as follows:
> m <- cateGOry(go$refseq_dna, go$go, FALSE)
Error in augmentByAncestors(ux) : GO terms 24, 172, 1978, 1979, 4442...Neither
worked.
Any idea? Thanks, Oleg
> index <- c(24, 172, 1978, 1979, 4441)
> m <- cateGOry(go$refseq_dna[-index], go$go[-index], FALSE)
Error in augment…
How do I add ME labels (ex. MEcyan) to the left hand side of my eigengene adjacency heatmap? I’ve seen this figure produced in publications. Is there an argument for...How do I add ME labels (ex. MEcyan) to the left hand side of my eigengene adjacency heatmap? I’ve seen this figure produced in publications. Is there an argument for the...setMargins=TRUE, plotHeatmaps=TRUE, plotDendrograms=FALSE)
…
This is a request for comments on planned changes to the ensemblVEP package. The intent is to provide lightweight wrappers to the ensembl VEP REST...API and to deprecate most of the software in the package.
Users of ensemblVEP may respond with comments to this post to describe their use cases. As examples of new approaches emerge in development, I will post more details
updated 24 months ago • Vincent J. Carey, Jr.
go to http://www.bioconductor.org/help/course-materials/ (also accessible from our home page as the "Recent courses" link in the "Learn" box) Courses are searchable and sortable by keyword, course name, title, date, and more. Thanks...to everyone who attended BioC2014 and gave us feedback which prompted this change.
Dan
updated 11.3 years ago • Dan Tenenbaum
<div class="preformatted">Hello bioC users,
as you can see below, this was posted over a year ago. Unfortunately I
tried the same today and for some mysterious it is not working
correctly
any more.
What I have is the same data.frame:
> dat
id flybasename_gene flybase_gene_id entrezgene
1 1616608_a_at Gpdh FBgn0001128 33824
2 1622892_s_at CG3…
div class="preformatted">Hello,
I was wondering whether anyone could suggest sources of information
about amplified genes in cancer, especially if the website tries to
combine it with (over)expression...information. We wrote a review on
amplified and expressed genes recently and are trying to get a sense
of
what else is out there, so that when we update it we make sure we get
different sourc…
builds[index], sep
= ""), :
unable to open connection
Is it because that GO has changed its downloading address from:
"http://www.godatabase.org/dev/database/archive/latest"
to
"http://archive.godatabase.org
the best way to proceed in this case. "Level1" individuals become "level2" individuals because they change behavior throughout their lifespan. Perhaps that "level2" individual had very recently transitioned from "level1...that "level2" individual as "level1", or perhaps consider "level1 + level2" individuals as a single category and compare against "level3", since I'm mostly interested in the gen…
I had written to do GO
analysis using the package GOstats, and to do this by switching to
package Category. I wanted to add KEGG testing to the GO testing I
have
been doing. All I did to my code was to add a conditional such that...if
the category was KEGG a KEGGHyperGParams object would be created, else
if it was BP, MF, or CC a GOHyperGParams object would be created...Then
the object params wou…
updated 17.8 years ago • Mark W Kimpel
div class="preformatted">Hi,
Instead of using GO or KEGG categories, is it possible to use
customerized categories. For example:
CC1 : gene1, gene2, gene3
CC2 : gene4, gene5..
instead of
GO1...gene1, gene2
I am just wondering which package allows me to give my own defn. of
categories.
For this purpose, I made a code from basic Hypergeometric {stats} by
using dhyper. But what I got is prob…
<div class="preformatted">Dear List
I want to do a hypergeometric testing of GO, KEGG and PFAM terms. I'm
using
the GOstats package and the method described in the vignette: "How to
use
GOstas and Category to do hypergeometric testing with unsupported
model
organisms" by M. Carlson, Oct. 31. 2011, because my organism is a...I'm
using
the GOstats package and the method described in the vign…
updated 14.1 years ago • Henrik De Fine Licht
shorter lines; 501 lines (14%) are > 80 characters long.
Most of these lines are roxygen comments.
formatR package says :
> Also note that single lines of long comments will be wrapped into
> shorter ones automatically...when wrap = TRUE, but roxygen comments will
> not be wrapped (i.e., comments that begin with #').
Don't tell me I have to do this one l…
updated 4.3 years ago • ZheFrench
numbers of genes per GO category.
__\#\#\# Approach 1 \#\#\#__
<pre>
> library(goseq)
> gene.vector = as.integer(assayed.genes%in%de.genes) #19,792 total genes (502...bosTau4", "ensGene")
> GO.hiper = goseq(pwf, "bosTau4", "ensGene")
> GO.hiper[GO.hiper$category=="GO:0005509",]
category over_represented_pvalue under_represented_pvalue numDEInCat numI…
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Answer: How to do differential expresion across time serise with edgeR?
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