and discussion;
be
prepared with a modern laptop, R-2.14, and additional software
packages
to be identified prior to the start of the course. There are a limited
number of positions available, so register early!
Likely topics
Order by: Relevance
and test sets the same data in order to check the robustness of module definition. The sizes of the identified modules are: 82, 88, 89, 114, 177, 177, 915, 1064, 1162, 1272, 1692, 2045, 3248. So, I have read in the paper titled...that the Z statistics and permutation test p-values often depend on the module size (i.e. the number of nodes in a module). This fact reflec…
seems to be lost, such that for the staining controls ('DNP
(High)', 'Biotin (Med)') I just get identifiers like STAINING,
STAINING.1. The results of methylumi's qcplot() function are then
supremely un-useful. Likewise...The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
</div
updated 12.4 years ago • Jon Manning
<div class="preformatted">Hi,
Apologies for the long list of questions, I have searched the mailing
list but can't find much info about these arrays.
I am looking at low density PCR cards. They measure the expression
levels of 96 different transcripts from a very small sample of human
or
animal tissue. There are actually 384 reactions going on but in our
case
each is done in quadruplicate…
updated 17.3 years ago • james perkins
for your email. The results you are seeing are expected.
The goal of the BrainArray mappings is to identify high-quality probes
and
to enable mapping of individual probes to genes (rather than
Affymetrix
probesets). On HG...U133A, BrainArray indicates that only 12,079 genes
have
an adequate number of high-quality probes to generate a reliable
summarized value. Please let me know if that doesn't …
as an intern to contribute to developing computational algorithms and methods for detecting copy number variation (CNV) in cancer, using next generation sequencing data. This is a part time paid internship for 15-20 hour...The position begins January 15th 2015 and ends July 15th 2015.
__Responsibilities__
* Identify characteristics and limitations of current CNV …
updated 11.1 years ago • Doe, Aimee
and limma to normalize the data and then fit the linear method (creating an object 'fit') that can identify the most expressed genes. The data come from the example.lumi dataset contained in the package lumiBarnes.
I then...fit <- eBayes(fit)
# print most expressed genes
topTable(fit, coef='95:5-100:0', adjust='fdr', number=10)
# volcano plot
gene_list <- topTable(fit, coef='…
updated 8.3 years ago • marongiu.luigi
Hello,
I am encountering an issue with the "Graphics API version mismatch" error when using the DESeq2 package in RStudio on Ubuntu 22.04. The error occurs when attempting to save...DESeq2 functions like plotPCA. I have thoroughly investigated this issue, including checking package versions, graphics drivers, and system settings, but I have not been able to find a resolution.
Environment:
R ve…
regardless? Thanks!
p.s. Sorry, I'm still very new to R....
Here is my session info:
<pre>
R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS
updated 7.4 years ago • gradypierroz
will be reproducible with any data you have lying around.
Thanks.
E: just to add, this is on version 1.6.4, the command would have been something very much like: `subread-align -r $file -R $file2 -i $index -t 0 -P 3 -T 1 -o $out`. It wasn
when running the DesignPrimers function of DECIPHER. I’m running DECIPHER v2.16.1 in R v4.0.2 and R version 4.1.0.
I have also installed the OligoArrayAux program which is accessible by the system (see below).
```
system("hybrid...lt;- system.file("extdata", "Bacteria_175seqs.sqlite", package="DECIPHER")
tiles <- TileSeqs(db, identifier=c("Enterobacteriales","Pseudomonadales"))
prim…
updated 4.3 years ago • Mailys
sample
code:
>###################################################
>### code chunk number 11: math2
>###################################################
>lena4 = lena[299:376, 224:301]
Error in slot(lena, ".Data")[299:376, 224:301] :
incorrect number of dimensions
>lena5...S3 to S4 that changes the way this code should
be written?
Thanks,
Rob
[[alt…
<div class="preformatted">I am reposting to the mailing list as it was bounced the first time.
Sorry if you received this more than once.
Best,
Norman
---------- Forwarded message ----------
From: Norman Pavelka <normanpavelka@gmail.com>
Date: 2011/9/22
Subject: Re: Help on PLGEM R Package Data Import
To: Wu Qi <qwu at="" dicp.ac.cn="">
Cc: bioconductor at stat.math.ethz.ch, m…
Dear all,
I'm trying to use biomaRt to map the chromosome location to gene ID,(
I got chromosome number, start position and stop position, and it's
for human)
May I ask the syntax of it?
Many thanks
YAn
[[alternative HTML version
When I tried to install the package clusterProfiler in R (version 3.4.1), I met some problems which are listed as follows.
Do you have any suggestions?
Thank you.
\#\#\#\#\#\#\#\#\#\#\#
## __> library...loaded
ERROR: lazy loading failed for package ‘DO.db’
\* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/DO.db’
…
updated 8.0 years ago • fengleiluck
<div class="preformatted">Hi,
I am encountering an error when attempting to retrieve data from the X
chromosome using GViz. The error is unclear to me and I would greatly
appreciate some help.
The code and error and sessionInfo() are below. Please note that I
have tried the code with and without ucscChromosomeNames=FALSE.
Thank you very much.
best wishes,
Chris
CODE:
################…
<div class="preformatted">yes Gregory..
On Tue, Oct 1, 2013 at 2:36 PM, gregory voisin <voisingreg@yahoo.fr>
wrote:
> Hi if I understand well: you have 1 cel for the control and 1 cel
for the
> experiment.
> You have no replication?
>
>
>
>
> ------------------------------
> *De :* deepika lakhwani <lakhwanideepik…
updated 12.2 years ago • deepika lakhwani
here:
http://bioconductor.org/checkResults/2.4/bioc-LATEST/
Note that these are the developmental versions of these packages. The
release version of GenomeGraphs should also be fixed (version 1.2.1)
but
this is not yet available...the
next 12
hours).
Also note that the release branch of biomaRt should be used with the
release version of GenomeGraphs and the devel version of biomaRt
should be
…
updated 17.0 years ago • steffen@stat.Berkeley.EDU
Hi all,
I know this was discussed already, but still after reading a lot here and in the vignette, I'm still not sure, I am doing it correctly.
I have multiple time points (colData below) with two or three replica. I am interessted in finding genes which are differentially regulated between two specific time points (TP) and also such, which are DE over all TP.
This is what I have done so far:
…
updated 10.2 years ago • Assa Yeroslaviz
gt; wild.fish
AffyBatch object
size of arrays=712x712 features (10 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish
notes=
> Dicer.fish
AffyBatch object
size of arrays=712x712...features (10 kb)
cdf=Zebrafish (15617 affyids)
number of samples=3
number of genes=15617
annotation=zebrafish
notes=
Now, I have to combine these two S4 objects and …
updated 14.8 years ago • Sukhbir Rattan
an Illumina provided csv file
with the probe/target sequence information, or use the older packages
(version matched):
lumiR("test_sample_gene_profile.txt", lib="lumiMouseV1")
I happen to have many files from this version of BeadStudio...package)
Any comments or suggestions would be greatly appreciated...
Cheers,
Cei
sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1
locale…
updated 17.6 years ago • Cei Abreu-Goodger
I tried using the processAmplicons function from edgeR where the hairpin sequence is at start in the fastq file and the barcode towards the end. While there are 100% matches with barcodes, I'm getting 0% for the hairpins. However the hairpin sequences are present in the fastq file. As the updated version of this function now allows both structured and variable structures I am not able to specify …
updated 3.4 years ago • Claire.Prince
undefined columns selected
I suspect GenePix 6 have some new columns different than previous
version:
Block Column Row Name ID X Y Dia. F635
Median F635 Mean F635 SD F635 CV B635 B635 Median
B635 Mean B635 SD B635 CV % > B635
updated 20.2 years ago • Ye, Bin
div class="preformatted">Dear List,
I wonder what is the correct probe identifier for illumina annotation
packages.
I have the illumina raw data (tiff) where the beads are identified by
their corresponding...use the illuminaRatv1 annotation package. And
my question is, how can I map Array_Address_IDs to the identifiers of
the annotation package.
I read in several postings in the List, that …
updated 17.4 years ago • Michal Kolář
We have been using justRMA to generate RMA values for some time.
Recently we
noticed that the latest versions of R(2.4.0/2.4.1) together with
BioC(1.9)
gave very different RMA expression values. Just wondering if anybody
else
updated 19.0 years ago • Quanli Wang
Dear Dr. Ou,
It seems that the interactive version of trackViewer can't handle negative values in bigWig files. Here is an example track in bigWig format: https://www.dropbox.com
updated 6.4 years ago • liruiradiant
t say that they divide after sum up...I was wondering if i need to divide the raw counts by the number of technical replicates added because it will have an impact on the size factor ?
Thanks
updated 9.2 years ago • ZheFrench
Dear all.
The firstSigNodes argument in the function that plots DAG in topGO allows to control the number of "TOP ranked" significant GO terms that will be including in the DAG. However the problem is that parents GO terms are
it is exposed to
two conditions (treatment and control).
- I've managed to derive a list of genes identified as differentially
expressed. As a result, I have two .txt files: one containing a column
of the original complete...list of probes/genes involved in the
experiment and one containing a column of probes/genes identified as
differentially expressed.
Is it possible to implement GOstats proce…
s just this particular data set that seems to be getting the error. This data set does have a large number of samples (155) and a small number of genomic features (13 bacterial orders), so I'm not sure if those dimensions are part...estimateDisp(dge, design)
fit = glmQLFit(dge, design)
```
Here is the sessionInfo():
```
R version 4.5.2 (2025-10-31)
Platform: x86_64-apple-darwin20
Runni…
updated 9 days ago • Mark
the spinal cord has already undergone some changes: for example, death of neurons. I would like to identify which alternative splicing events are independent of changes in cell type composition, both because these are...reflects the force delivered in kDyn and is modeled as a continuous covariate.
In order to identify AS events that are independent of cell type composition, I am trying to follow…
updated 6.9 years ago • skinnider
109525 ] found.
Searching in chrW ...[ 17866 ] found.
Searching in chrZ ...[ 815671 ] found.
Number of identified CG pattern: 10689093
Calculating genomic coordinates...
Creating Granges object for genome wide windows...Counting the number of CG's in each window...</pre>
When I try to use the mr.edgeR to calculate differencial coverage between two conditions...results =…
SNPs.
I got genotypes with as a flat file with affy IDs for the snps and I
would
like to have the rs numbers for those
Best Regards
Marco
[[alternative HTML version deleted]]
</div
updated 17.4 years ago • marco zucchelli
wrong. If I rename the samples of a LumiBatch object, I can
no
longer subset them by name (with numbers it still works). Here's an
example, followed by my sessionInfo.
library(lumi)
data(example.lumi)
# This works
example.lumi...subscript out of bounds
==================================================
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1
locale:
C
atta…
updated 17.7 years ago • Cei Abreu-Goodger
I've got a question concerning the GO.db package, in particular about the annotation of GO identifiers to their parents. I read the pdf that describes the functions of GOMFPARENTS, GOCCPARENTS and GOBPPARENTS and...gene ontology consortium website. There is a graph that shows, that this node has two parents: node number "GO:0016772" and number "GO:0016310". Now, if I do in R:
<p…
updated 11.2 years ago • 1frcn
gt; please could you let me know whether there is any command in R/BioC
that
> would allow to identify long consensus sites (16-20 nt length) in a
set of
> DNA sequences.
>
> Thanks a lot !
>
> Arici
>
> [[alternative HTML...version deleted]]
>
> _______________________________________________
> Bioc-sig-sequencing…
updated 16.1 years ago • Wolfgang Huber
all isoforms and it
would be difficult to get the coordinates for the most common isoform.
How can I identify the most common isoform?
many thanks!
[[alternative HTML version deleted]]
</div
preformatted">Hi,
Firstly thanks to the creators of this very useful package.
I've come across SRA identifiers that don't appear to be in the
database (a
minority, but still). Here's a few:
SRA036600
DRX001436
SRA049463
ERA062401...recent SRA
submissions in the SRAdb).
Any ideas?
Thanks in advance,
ben
[[alternative HTML version deleted]]
</div
updated 13.6 years ago • Ben Woodcroft
an XML file but
I
don't see an easy way of mapping the proteins to ENTREZ IDs or similar
atomic identifiers. Has anyone written any code to parse this?
Thanks,
Fraser
[[alternative HTML version deleted]]
</div
well as to
test for differentially methylated probes/positions (dmps). However, I
would also like to identify
differentially methylated regions (dmrs) and have tried the
MethyAnalysis package for this.
Does anyone know how...Unit
Level 7, Addenbrooke's Hospital
Hills Road, Cambridge, CB2 0QQ
[[alternative HTML version deleted]]
</div
updated 12.8 years ago • Matthias Zilbauer
gt; ddsEmbF
class: DESeqDataSet
dim: 42761 1528
metadata(1): version
assays(1): counts
rownames(42761): 5S\_rRNA 7SK ... snoZ6 yR211F11.2
rowData names(0):
colnames(1528): E3.1.443 E3.1.444 ... E7.9.573
updated 9.4 years ago • b.cox
it would be great if you can let me know. Thank you in advance!
The purpose of the project is to identify downstream targets of a few plant transcription factors (let’s call them gene A,B,C,D,E,F) that are essential for colonization...colonization-induced genes in WT because it's the reference level, but 410 is much less than the number I expected. If I directly compare WT_Inoculated vs WT_Mock …
updated 4.1 years ago • tiansy
div class="preformatted">Hello,
Does anyone know if Biostrings is being maintained? I see the version
number bumped between Bioconductor releases, but the maintainer's
(Saikat Debroy) e-mail bounces at the University...amino acid strings. It
seems to be partially implemented, so I wonder if anyone else has a
later version than is to be included in 1.8.
Alternatively, if anyone knows of an …
updated 20.2 years ago • Marcus G. Daniels
Hi,
I am using version 1.16.1 of DESeq2. According to the documentation, a Cook's distance cutoff of 0.99 is applied to the results function...the source code in github and this certainly seems to be the case. However, if I get a larger number of significant genes when running the "results" function with default arguments compared to when I explicitly use...the ar…
updated 7.5 years ago • wpoehlm
to analyze my data. But the
Affy_ID
that naming the probesets have been replaced by gene accession numbers
(Atg-numbers in this case) in the new cdf-file and this makes the
annotation
from Bioconductor useless to me: the keys...used there are Affy_IDs.
So obviously I have to make new mappings from gene accession numbers
to e.g.
GO-terms, but that information is available on databases.
*My quest…
updated 17.6 years ago • Samuel Wuest
div class="preformatted">Hi, all; I've got a large number of expression values that are
currently associated with the old 2004 rat genome build RefSeq IDs,
and unfortunately...have updated to the new RefSeqs and I can't seem to
link back to the old ones. I think an old version of org.Rn.eg.db
would do the trick but the current version is also updated. Is there
any way to get an older version
biomaRt to convert Affy probes to HUGO gene names. Using the same set of probes, I got a different number of genes last month using the previous version of biomaRt, and I get slightly less genes now with the current version...mapping, and I want all my data to be consistent. Is there a way to access (install) the previous version of bioMart (the one I used on March 8th)?
Here is my conversion co…
updated 10.5 years ago • ebrudermanver
Hello,
I am interested in finding differentially spliced genes using the `diffSplice` function from the `limma` package.
For example, in the code below, Gene1 shows the most evidence of differential splicing, with Exon1 being significantly more highly expressed than the other Gene1 exons, when comparing group 2 to group 1. However, for such a differentially spliced gene, I would then like…
updated 4.4 years ago • jamie.gearing
Any suggestions and advice would indeed be valuable.
Thanks.
Chintanu
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
attached base packages:
[1] splines tools stats graphics grDevices utils
datasets...show (Data_A)
AffyBatch object
size of arrays=712x712 features (8 kb)
cdf=HG-U133A (22283 affyids)
number of samples=14
number of genes=22283
annotation=…
I successfully pushed updates of package RiboDiPA to bioconductor with version bump, but didn't receive automatic notification from bioconductor. Any clues on why
updated 4.0 years ago • Jiping Wang
<div class="preformatted">Dear Alex,
You have just rediscovered one of the problems of classical testing -
when the sample size is large, you have the power to detect
differences that are statistically significant, but have no practical
importance. The answer here is to filter on a threshold of
differential expression which you consider to be important in
addition to statistical significan…
gt; source("http://www.bioconductor.org/getBioC.R")
>
> getBioC(develOK=TRUE)
Running getBioC version 1.2.64....
If you encounter problems, first make sure that
you are running the latest version of getBioC()
which can be found...get time I'll update. Last time I checked c. 1
> > month ago - the R devel was still the same version. I'll
> check again.
>
&a…
Dear,
Currently, I would like to calculate exon counts using package Rsubread 1.32.0, function featurecounts.
Inputs:
1. Bam file based on paired end RNA sequencing.
2. Annotation file in GTF format, downloaded from GenCode v27.
*More details about Bam:*
- Created based on uBam.
- Aligned with Star
- Unmapped reads are kept in/ added to bam
- File is validated multiple time…
updated 6.7 years ago • edejong
Hi everyone,
I'm trying to use DESeq2 to analyze some mutagenesis data and identify variants that confer a selective advantage. To do so, I'm comparing the counts of thousands of mutants before and...Hi everyone,
I'm trying to use DESeq2 to analyze some mutagenesis data and identify variants that confer a selective advantage. To do so, I'm comparing the counts of thousands of mutants before and…
updated 7.2 years ago • Thomas_WILLEMS
I'm trying to use CopywriteR to identify copy number alterations from .bam files, obtained using whole exome sequencing on a set of 30 human cancer tissues
updated 4.2 years ago • Joshua
to take both into account?
Basically I'm not just interested in the top 50 genes, I'd like to identify all 'significant' changes. I thought the output from `classifyTestsP` (0.01, fdr) would be good but this doesn't account...con.fit <- contrasts.fit(fit, cont.matrix)
ebfit <- eBayes(con.fit)
topTable(ebfit,coef=1,number=50,adjust="fdr")
```
Thanks alot,
Matt
updated 6.9 years ago • Matthew Hannah
<div class="preformatted">
Hello all,
I am trying to map a set of Genbank accession numbers to LocusLink IDs
and
get the following error using humanLLMappingsACCNUM2ALL:
> get("AF426250",humanLLMappingsACCNUM2LL)
Error in get("AF426250", humanLLMappingsACCNUM2LL) :
recursive default argument reference
I can map the other way from locuslink id to accession number, for
exa…
updated 20.8 years ago • Denise Scholtens
you noted in the DESeq vignette, but
this
is all I have.
What I am finding it to be odd is that the number of DE genes I get
from
doing the pair-wise DE detection for 6 samples does not negatively
correlate with the Pearson...6 samples (I.e. I expected that
libraries with the higher correlation coefficient would have less
number
of DE genes. But this is not what I am seeing.).
I am looking for y…
<div class="preformatted">Hi,
I am using hclust and cutree to cluster a data frame y and cut it
into few
clusters as follows
y
V1 V2 V3 V4
A 1 2 3 4
B 5 6 7 8
C 9 10 11 12
D 13 14 15 16
E 17 18 19 20
> clu<-hclust(dist(y),method="complete")
clu<-hclust(dist(y),method="complete")
> clu
Call:
hclust(d = dist(y), method = "complete")
Cluster method …
updated 11.7 years ago • chris Jhon
making a karyogram with ideograms
of
each chromosome? I have looked at GenomeGraphs, Idiogram and a number
of
other packages but they seem like they have been designed to draw a
single
chromosome at a time. Ideally, I would like...to
be able
to illustrate multiple features (ie. one might be genes, a second
might be
copy number variations or single nucleotide polymorphisms).
Thanks,
Michael Go…
updated 17.5 years ago • Michael Gormley
Recent ...
Replies
Answer: blockwiseModule crashes in the end and doesn't generate modules
by
Daniel
•
0
Queria compartir mi experiencia con [https://jugabet.cl/football/live/1][1]
. Esta seccion ofrece cobertura en vivo de futbol, con marcado…
Comment: Empty boxes in treemap plot rrvgo package
by
TikTsokaasocissalpc
•
0
Clear visualization matters just as much in mobile entertainment as in data analysis. The [Try KK33 Game App now][1] focuses on clean layou…
Comment: nice 3D displays for PCA analysis
by
adam80haynes
•
0
That's a fascinating application of 3D printing in a scientific context. Using this technology to create custom lab equipment, models of mo…
Comment: Bioinformatician at the Lausanne University Hospital
by
TikTsokaasocissalpc
•
0
The Random Word Generator in Italian is a useful tool for generating ideas and exploring new approaches, much like the innovative research …
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
TikTsokaasocissalpc
•
0
If you want to share your research progress and microbiome discoveries with colleagues or friends, [snaptroid android][1] download free mak…
Votes
Awards
• All
Popular Question to
Gordon Smyth
53k
Popular Question to
Hervé Pagès
16k
Popular Question to
Istvan Albert
▴
50
Popular Question to
Dario Strbenac
★
1.6k
Locations
• All
United States, 39 minutes ago
The Netherlands, 1 hour ago
Türkiye, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
India, 2 hours ago
United States, 39 minutes ago
The Netherlands, 1 hour ago
Türkiye, 1 hour ago
WEHI, Melbourne, Australia, 1 hour ago
India, 2 hours ago
Traffic: 1340 users visited in the last hour
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by the
version 2.3.6
version 2.3.6