div class="preformatted">
With a recent update of bioconductor it appears to me that a little
bug has
been introduced into plotMA() in the limma package:
Selecting...with plotMA(foo, array=2) does not work
anymore if foo is an RGList.
The reason seems to be a small change in the respective part of the
source code
from
MA <- MA.RG(MA[, array])
array <- 1
in limma 2.12.0 (2…
Order by: Relevance
this useful package.
Gviz seems to put transcriptAnnotation labels of gene model tracks only on the left side. Since I need to represent the 3'UTR region, I don't have labels in my plots, so I would like to show the transcriptAnnotation
updated 4.4 years ago • mar.pieraccioli
I would like to colour a dotplot of top 20 enriched biological processes by the median fold change of the genes in each category. The fold change of all genes in the enrichment analysis are provided by a separate vector...style list that has entrez IDs associated, fold changes are from an experimentally derived dataset. I think this requires some workaround. Thanks in advance for your help
updated 3.7 years ago • Colin
which I have already processed, I now have a list of up and down-regulated genes with p-values, fold changes, and KO numbers (already ran proteins through KEGG) which contains about 850 genes. I want to run this data through...Gage/Pathview to look at any metabolic pathway changes which have occurred under my specific treatment. The gage and pathview vignettes are not commente…
<div class="preformatted">Dear Bioconductors,while re-running the basic rma protocol on some
Affy mouse exon arrays (Mouse Exon 1.0 alias MoEx-1.0) I noticed that
all at sudden I get 1201338 exons(/elements) instead of 1411189 in Oct
2007. Since the R and the BioC release(s) changed, however, the
annotation package (on www.bioconductor.org) is still the same (i.e.
mouseexonpmcdf_1…
updated 17.5 years ago • Wolfgang RAFFELSBERGER
Hi Michael and everyone,
We did a simple tutorial for students and detected a strange behavior.
Changing just a single count in a table of 1000 genes changes adjusted P-values from ~0.98 to more expected in range of 10^-6 ~ 1:
Line...packages/release/bioc/src/contrib/DESeq2_1.34.0.tar.gz"
#install.packages(url, repos=NULL, type="source")
library(DESeq2)
packageVersion("DESeq2")
# Se…
updated 4.1 years ago • Andrey
hyperGTest(params)
Error in getUniverseHelper(probes, datPkg, entrezIds) :
No Entrez Gene ids left in universe
Thanks,
Ben
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: universe.txt
URL: <https
is dated on Dec 18, 2005, and the rest
is
on March 18, 2006.
We treat the first two as "trust" sources, and the last two as
supplimentary sources. So, the supplimentary sources won't be used
unless all the "trust" sources...have missing values for a probeset. No
matter whether we use "trust" or "supplimentary" sources, if there is
disagreement on the mapping of a probeset, we pick the value that…
updated 19.6 years ago • Nianhua Li
<div class="preformatted">(I recently posted an empty message with almost the same subject. I
tried to resend it, but unfortunately our email servers were down.
Here
is an updated version).
I am looking at expanding the image methid for an AffyBatch object, in
the sense that I only want to plot certain (x,y) coordinates. I ahve
therefore looked at the code and have a little problem underst…
updated 20.8 years ago • Kasper Daniel Hansen
too is
"paralog". When talking about genes, these terms describe what we know
about the evolutionary history of a gene. Homologous genes are related
to each other by having the same common ancestor. Homologs can be
further divided...s
Throughout the vignette, the term "ortholog" is used in error and
should
be changed to "homolog" - in all cases (without checking the context
of
every occurrence).…
updated 17.5 years ago • Nathan.Watson-Haigh@csiro.au
you explain the purpose of maxInt? What exactly is it doing? The manual says "Maximal length of the left and the right segment. (Default = 40).
But the source code shows fastseg calls another internal function segmentGeneral
updated 9.3 years ago • epic4benjis78
class="preformatted">Hi,
I just want to know if it is also possible to
test for underrepresented GO categories by
using the weight algorithm. If yes, do I have
to change something in the definition of the
test statistic when
Hi,
I have the following RNA-seq experiment:
control (right tissue) vs control (left tissue)
case (right tissue) vs case (left tissue)
I would like to find the DE genes present in the first comparison + DE genes...comparison but discarding those DE genes that are significant in both comparisons with the same fold change direction. The way I proceed is to perform DE analysis for each compariso…
updated 8.7 years ago • aec
reps of untreated (U) and treated (T),
normalised by RMA
and in this case looked at 2 fold changes. I made the U-T pairwise
comparison for
each replicate and counted the number of genes where fold change >2.
To assess...1rep 2rep 3rep
U-T 1544 1201 1008 These are the changes
due to treatment
U 31 13 1 …
updated 21.9 years ago • Matthew Hannah
div class="preformatted">Hi! My name is Yeon-Ki.
I tried to see the C source code for normalize.method="qspline",
in the method expresso in affy package.
Could somebody show me how to see the C source
example
there are 30 Go clasess that appear.
I then conduct Fisher's exact test 30 times on each GO category to
detect
differential representation of terms in the expressed
set and correct for multiple testing.
My question
div class="preformatted">I installed the R-package from source code in a linux readhat 7.3. The
program runs. The problem is when I tried to install (or update) new
packages and libraries...message:
**********************************************************************
**
*********
> source("http://www.bioconductor.org/getBioC.R")
> getBioC(relLevel="release")
Running getBioC…
updated 22.1 years ago • Roger Vallejo
<div class="preformatted">
Hi again,
First, I'd like to say thanks to everyone who's sent comments
or suggestions on this. I've now managed to sort the problems out but
just wanted to reply to a few of the questions raised...div class="preformatted">
Hi again,
First, I'd like to say thanks to everyone who's sent comments
or suggestions on this. I've now managed to sort …
hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/geneXtendeR</pre>
2) Now make the necessary changes to your package. E.g., add your new files in by copy/paste or drag-and-drop into this directory that you downloaded...version from x.y.z to x.y.(z+1) in your package’s DESCRIPTION file. If the version is not properly changed your changes will not be made available in the Biocon…
updated 8.4 years ago • Bohdan Khomtchouk
div class="preformatted">Dear All,
Following some recent data analysis, we constructed a short tutorial
on analysing time-course microarray data. You can access this tutorial...ncsg3/microarray/
The document was constructed using Sweave, so all R code is available.
Any comments/suggestions welcome - probably directly to me and off the
list would be best.
Best wishes,
Colin
--
Dr Colin Gi…
updated 15.8 years ago • Colin Gillespie
div class="preformatted">Dear All,
Following some recent data analysis, we constructed a short tutorial
on analysing time-course microarray data. You can access this tutorial...ncsg3/microarray/
The document was constructed using Sweave, so all R code is available.
Any comments/suggestions welcome - probably directly to me and off the
list would be best.
Best wishes,
Colin
--
Dr Colin Gi…
updated 15.8 years ago • Colin Gillespie
was on a separate flowcell etc). I am looking at how each transcription factor's binding affinity is changing in disease vs. normal. As such, I will be using DBA\_REPLICATE as a blocking factor when I look at differential TF binding...the Tissue metadata column of the sample sheet), is there a need to set up a blocking factor if the category being used for dba.contrast() is the tissue type i.e no…
updated 7.3 years ago • Mthabisi Moyo
with
their GPL IDs, I was wondering if someone could tell me how to get the
information on what the source file is for a package? For example,
I'd
like to know what the source file is for the package
'MmAgilentDesign026655.db...I'm presuming that this is in the source file used to generate the
Bioconductor package, but I'd like to check that is the case. What do
people usually do about
div class="preformatted">I recently tried to install the iFlow flow cytometry GUI on top of my
R/Bioconductor installation, and received a warning message...Gabriel Kaufman
McGill University Complex Traits Group
-------------------------------------
> source("http://bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
> biocL…
I have a dataset with 10 condition vs 20 control samples and am using limma to test for differential expression. Broadly, groups are age/sex matched but have complex medical histories which add noise to the condition vs control comparision.
Ideally, I'd just have a higher n and cleaner cohorts, but that isn't an option. Currently I'm currently controlling for one aspect of the medical history …
updated 12 months ago • Ali Barry
This is BiocCheck version 1.15.9. BiocCheck is a work in progress. Output and severity of issues may
change. Installing package...
\* Checking if other packages can import this one...
\* Checking to see if we understand object initialization...Checking for non-trivial biocViews...
\* Checking that biocViews come from the same category...
\* Checking biocViews validity...
\* Chec…
updated 7.7 years ago • topijush
<div class="preformatted"> Hello Bioconductor Users,
Sorry to bother you, but I have a couple of quick questions on the
affy package that I have been unable to answer by reading through the
textual description of affy available on the bioconductor website and
the recent papers on the subject. Iin general, am very impressed with
the noise reduction using affy and truly appreciate the Bioco…
updated 22.8 years ago • Luckey, John
<div class="preformatted">Hello Bioconductor Users,
Sorry to bother you, but I have a couple of quick questions on the
affy package that I have been unable to answer by reading through the
textual description of affy available on the bioconductor website and
the recent papers on the subject. Iin general, am very impressed with
the noise reduction using affy and truly appreciate the Biocond…
updated 22.8 years ago • Luckey, John
<div class="preformatted">
Thanks Tom, Sean, Xavier for the reply, and especially Adai!
However I still have a problem. To put the microarray data into these
supervised clustering, the expreSet need to be built. To build
expreSet, you need to give the class of every sample. So when I
predict samples with unknown classes, how to put them into the
expreSet? Thank you!
Xin
-----Original Mess…
updated 21.5 years ago • Liu, Xin
to review our report prior to its submission to the NIH. Please complete your review and post comments by November 1, 2014.
The link to the report is here: <a href="http://softwarediscoveryindex.org/" target="_blank
bamdata,file="bamdata.tbl",sep="\\t")
<span style="line-height:1.6">But, when I change "refSeqName" and call cn.mops function:</span>
bamDataRanges <- getReadCountsFromBAM(BAMFiles,mode="paired...Starting segmentation algorithm...
Using "fastseg" for segmentation.
No CNVs detected. Try changing "normalization", "priorImpact" or "thres…
updated 9.3 years ago • Ponyo
class="preformatted">Hello ...
Due to the proliferation of data sets, I've taken them off of the left
hand frame and given them their own page. You can now access the data
via
the website using the "Data" link, which is just below...data can still be accessed directly using the same URLs as before,
only the HTML presentation has changed.
-J
</div
updated 23.5 years ago • Jeff Gentry
Hello everyone, I recently came across the MSGFgui packages for R (https://github.com/thomasp85/MSGFgui). I use command-line MS-GF+ regularly, but...httpuv_1.3.3 </pre>
It appears that MSGFgui is trying to get MSGFplus from a nonexistent source at UCSC. This seems odd, since I have installed MS-GF+ as a command-line program and (I think) as an R/bioconductor package
updated 10.1 years ago • Owen.Leiser
div class="preformatted">Hi all,
just a quick question: Having read Ben's comment on normalization
(only few
genes should change), I came to think of Affymetrix concept of using
100
genes which don't...change much as a normalization strategy. Has anybody
looked
into this / tried some R implementation?
Cheers,
hinrich d8-)</div
updated 21.8 years ago • Hinrich Goehlmann
split(as.data.frame(exprs(q)), sample.order)
Xnew <- do.call("cbind", X)
# Split categories
cats <- split(as.data.frame(featureCategory(q)),
sample.order)
catsnew <- do.call("cbind", cats)
# Split flags
flags...1]
featureClass(out) <-
featureClass(q)[as.numeric(sample.order)==1]
out at history &a…
solution. I have run GOSeq on my gene set and am looking to __identify the genes in each category (numDEInCat)__. Here is what I've done so far. After obtaining go\_bp as the result of running GOSeq:
`` head(go_bp...pre>
category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology
1667 GO:0006955 7.257450e
updated 8.5 years ago • krc3004
<div class="preformatted">Hello All,
I am trying to take advantage of some of the plotting options in the
qrqc package but I am getting an error (related to the "new" Illumina
quality scores) that seems to have come up last month (in the
archives). I tried to install with type = source but that did not fix
the error. Thanks for any suggestions.
Best,
Noah
> source("http://bioco…
updated 13.8 years ago • NDowell
preformatted">Dear all,
The new Ensembl marts for release 70 are live on www.ensembl.org.
You can change your host to access our most recent data:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
host="www.ensembl.org", path...Variation datasets have been renamed to "short variation (SNPs
and indels)".
Variation sources and Variation synonyms have been updated and
reorganised in…
There is currently a mismatch between the source (2.55) and binary (2.56) versions of the rGADEM package on the bioc release page.
Is this expected? Who can I notify to fix
updated 7 months ago • Jay hesselberth
When retrieving TCGA data using TCGAbiolinks, I am trying to find from where the column names are sourced and how they are decided e.g.
```r
colData(data)$paper_Telomere.Maintenance
```
or
```r
colData(data)$paper_Survival..months
updated 2.5 years ago • BioInfoBeginnerrr
Dear All,
I am trying to commit some changes to [bioCancer](https://github.com/Bioconductor-mirror/bioCancer). the issue is no changes added to commit.
Please, here...when you want to push your commits to svn
1. \`git svn rebase\` to get the latest SVN changes.
2. \`git svn dcommit --add-author-from\` to commit your changes to SVN.
* Change manually&am…
updated 9.5 years ago • kmezhoud
This is just a heads-up that, for the first time in several years,
I've
made a user visible change to the empirical Bayes procedure used in
the
limma package. I have changed the hyperparameter estimation to make it...are
now treated in a unified way. This means that eBayes() and topTable()
will
produce slightly changed signficance results for all data sets.
For most data sets the changes will be…
class="preformatted">Hi,
is there any way to retrieve the information about
the version/date of the source that was used for
the annotation package in addition to the date
for the generation of the package?
thank you very much
updated 18.9 years ago • Ido M. Tamir
<div class="preformatted">
Hi Waverley
In your input you also have Ensembl protein ids (e.g.
ENSP00000231338). You
could extract these, use them as your input list, use biomaRt to
match these
up with molecular function GO ids, calculate the frequency of the
ids, e.g
molecular_function%binding%protein binding 10
molecular_function%molecular transducer activity…
<div class="preformatted">Dear all,
After I updated the mzR package, I am unable to check or install my
package
due to 'shared object mzR.so not found' . I am including the whole
error
and my sessionInfo() below.
I thought it could be related to the recent changes as discussed in
the
thread entitled "mzR crashes R" and I have followed the discussion and
tried to re-install mzR in differ…
t-tests, this is what I do:
do.ttest <- function(y, x1=1, x2=2) {
# split y according to categories in pData
# For example you may have cell.line as a cateogry in pData
# because the function is called with esApply...it knows the
values of pData
# therefore knows that cell.line is one of the categories
# defaults for x1 and x2 are set as the first t…
Hi
I'm using a recent version of Enhancedvolcano and using data of 3 months ago where I got volcano plots with labels next to the points...Hi
I'm using a recent version of Enhancedvolcano and using data of 3 months ago where I got volcano plots with labels next to the points, today...I get labels that are right on top of the points. Is there a way to nudge these left or right top or bottom?
her…
updated 4.0 years ago • acharest
Hi,
I am thinking of using Rcistarget.
I will be using the databases linked below, what are the data sources for cisTarget databases?
[https://resources.aertslab.org/cistarget/](https://resources.aertslab.org/cistarget/)
For...I am thinking of using Rcistarget.
I will be using the databases linked below, what are the data sources for cisTarget databases?
[https://resources.aerts…
updated 3.7 years ago • th
Hi all,
I just wanted know whether Ringo(open source R package for ChIP-ChIP data)helps to analyze the Agilent Chip-chip data. And what are the INPUT file formats for the...Hi all,
I just wanted know whether Ringo(open source R package for ChIP-ChIP data)helps to analyze the Agilent Chip-chip data. And what are the INPUT file formats for the Ringo
updated 7.6 years ago • preranakoti93
<div class="preformatted">Hi,
I noticed this a while ago but with some of the recent threads, maybe
now is suitable for a general discussion.
This will be easiest if you view the attached files on the
bioconductor
archive site.
Basically GCRMA changed it's BG parameter estimation from using a low
quantile of strata of affinity levels (1.1.0 or less) to a smoother
way
using loess. There i…
div class="preformatted">Hi
I d like to compile the source code from last Affy package for
WinXPpro under
R18beta
however the doc is pretty poor regarding this process...
I went
output:
<code>GO.wall <- goseq(pwf, gene2cat = Biomart.GOdata)<br/>
head(GO.wall)</code>
<pre>
# category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology
# 962 GO:0003735 6.729949e...CC<span id="cke_bm_74E" style="display:none"> </span></pre>
However, wh…
updated 9.7 years ago • mrodrigues.fernanda
your
question
today.
CA is not the best approach for analysis of your factor table with 3
categories. It is designed for analysis of count data, originally for
analysis of contingency data (species x traits counts...to
ord
if you wish.
There are further methods available in ade4. If you can apply weight
to
the categories, there is fuzzy correspondence analysis dudi.fca, or if
you have a mix…
updated 19.4 years ago • Aedin Culhane
this been seen for other isoform data? As expected the isoform data points cluster strongly on the left side of the graph, while the gene-level data cluster more in the middle.
Thank you for any comments
a 2 tailed
equal variance t test?
I also thought I read that with such few replicates, a fold change
would be better than a t test?
If I get a t test of .0001, and a fold change of 1.2, is this a
reliable change using RMA?
Thanks
updated 22.1 years ago • Jason Hipp
I would like to announce that Affymetrix has released the PLIER
algorithm
SDK under a GPL open source license. The code is available as C++
without
windows dependencies. The SDK can be accessed at the URL below.
Documentation
The most recent CoGAPS Version 3.18.0 fails to install on my computer. Version 3.15.2 installs correctly.
I think this may be due to...questions/65966969/why-does-march-native-not-work-on-apple-m1
Is there any way to change the clang version used when compiling CoGAPS?
Thanks!
```r
Old packages: 'CoGAPS'
Update all/some/none? [a/s/n]:
a
Package which...is only available in sour…
with minOverlap=1 (all peaks to be included in the consensus peakset). However, dba.blacklist changes the consensus peakset to be based on minOverlap=2. How to run dba.blacklist without changing minOverlap?
```r
dbObj_blacklist...LC_MEASUREMENT=en_IL.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Jerusalem
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics…
updated 2.1 years ago • Sam
div class="preformatted">Dear Julien, Dear Mar and people interested in DEXSeq ,
You recently reported some problems in DEXSeq that had to do with the
way the HTSeq python scripts deal with the exons that overlap...the python scripts. These functions were implemented
using
code contributed by Mike Love.
All these changes are available in the last svn version (1.5.9).
Best regards,
Alejandro…
div class="preformatted">BioC List,
The pathview package was recently published in
Bioinformatics:
http://bioinformatics.oxfordjournals.org/content/early/2013/06/11/bioi
nformatics.btt285.full...http://pathview.r-forge.r-project.org/
Please try it out and let me know if you have any
comments/suggestions. Thank you!
Weijun Luo
</div
updated 12.5 years ago • Luo Weijun
Recent ...
Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴
10
Thank you @seandavi for your feedback.
I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★
4.1k
Hope you don't mind I am not Johannes... ;-)
Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
•
0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
•
0
Dear Johannes,
Would it be possible to generate a EnsDb for the newest Medicago V5 genome release?
Medicago truncatula A17 r5.0
This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴
80
When referring to the OSCA book including individual sub-books please cite the OSCA paper:
Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
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