the library from Bioconductor directly using the biocLite command and am currently running it in R version 3.3.3 “Another Canoe.”
When running the fgsea command the algorithm runs quickly (less than 1 second) for any number of
Order by: Relevance
list?
2. Using this command: summary(de <- decideTestsDGE(lrt))
is able to tell the total number of up-regulated and down-
regulated
genes/tags of the test. I would like to learn how can I extract these
up and
down-regulated...Thank you very much for your time and help.
Best regards,
KJ Lim
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</div
with limma.
When I do the analysis like in a factorial design (page 45 of the
manual) I
get a number of differentially expressed genes considerably lower than
when
I do separate channel analysis (page 50). From a biological...from a statistical point of
view. What do you think?
Thanks!
Luis.
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</div
updated 14.8 years ago • Luis A. Alcaraz
a way to find the answer after I
run
hyperGTest for hgu133a, hgu133plus2 and hgu95av2. I found the numbers
for
the three platforms are 637, 637 and 736. I don't know why the
databases of
GO terms are different for the three platforms...Did you always know?"
"No, I did not. But I believed..."
---Matrix III
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</div
updated 17.2 years ago • Weiwei Shi
level. I am assuming that the negative
binomial
model in some way accounts for tags with a large number of 0 cells.
Is
there something more going on the generalized linear model or in
fitting
the negative binomial distribution...percentage of
zeros from some of the tags?
Thank you for your guidance!
[[alternative HTML version deleted]]
</div
<div class="preformatted">
Hi,
After analysing my arrays for differentially expressed genes, I get a
list of genes Id. To reduce even more the number of genes in this
list, I would like to retain only genes related to the immune system.
I've looked for packages dealing with "ontology" but I couldn't find
any doing this simple task...
Any idea on what package/function I could use?
Thanks i…
updated 13.2 years ago • Guest User
hits$x, hits$y)
plot(bin)
Yields:
Error in cut.default(rcnt, colorcut, labels = FALSE) :
invalid number of intervals
However,
hits = list(x=rnorm(1000), y=rnorm(1000))
bin <- hexbin(hits$x, hits$y)
plot(bin)
Works fine. The thing is printing...data structure. Any ideas? Thank you.
--
Wells Oliver
wells@submute.net
[[alternative HTML version deleted]]
</div
gt; data
AffyBatch object
size of arrays=230x230 features (11 kb)
cdf=miRNA-1_0_2Xgain (??? affyids)
number of samples=5
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment...named "mirna102xgaincdf" from
BioConductor.
thanks
Xiaobin Yuan
[[alternative HTML version deleted]]
</div
updated 14.9 years ago • Xiaobin Yuan
to apply makePDpackage (from the MakePlatformDesgin
package) on the files of the Affymetrix 10k (Version 2.0) array.
I got the following error message:
Reading Mapping10K_Xba142.cdf
Magic number is not 67. This is probably
the length of the single
vectors
inside it. so to sayat the top are the ENTREZIDs with the largest
number of
probe IDs. (in my example $`10001` with 3, but I have some with
more!).
I tried with order and sort command, but that didn't work...THX in advance
Assa
--
Assa Yeroslaviz
Kockelsberg 22
51371 Leverkusen
[[alternative HTML version deleted]]
</div
updated 15.9 years ago • Assa Yeroslaviz
pheno=myPhenoData$Sample_Group, type="categorical")
and I've a variable number of significance estimates (qval < 0.05) on
the
two result objects.
In a dataset of 44 samples I've 207020 significance...So I was wondering which of the two result objects should I choose?
The one
with the greatest number of significance estimates?
In the manual shrinkVar=TRUE is recommended when sample sizes …
global scaling, or
> normalization, provided
> in the Affymetrix Microarray Suite software, version 5.0
(MAS5.0).
> 2. Since their methods reliably identify samples with an average
> intensity value of 30 or more but...gt; the data i download form NCBI GEO?
> Thanks in advance.
>
> [[alternative HTML version deleted]]
>
&g…
updated 20.3 years ago • Arne.Muller@sanofi-aventis.com
We had to switch to using `` bplapply() `` and in the later version of the package started to encounter serious performance issues. Here's an example using low number of cores (workers...0.196 0.020 9.953</pre>
<span style="line-height:1.6">bplapply time surges (proportional to the number of elements in the list).</span>
This is using BiocParallel\_1.2.22 (full se…
updated 10.0 years ago • peter.kharchenko
D microarray, and I have annotated the PROBEID via the "clariomdhumantranscriptcluster.db" for some identifiers.
However, some of the "ENSEMBL" (or other gene identifier) annotated probes does not have the corresponding transcript
updated 5.1 years ago • luca.piacentini
for loops, but the rownames for getGreen() and getRed() matrices from the RGChannelSet are numeric identifiers. I am unsure of how to go about identifying which channels go to which array probe.</span>
I am running minfi 1.18.6
some sets of genes I wish to test for enrichment against a
background set of genes. These genes are identified by Ensembl
identifiers. I have found it quite straightforward to use the topGO
package to do this.
I would also like
updated 17.6 years ago • John Reid
Type of Gene ID: no gene ids ``
In the third case (knownGene), I get Entrez Gene ID numeric identifiers. Is there a way to get the standard gene name identifiers? Assistance/advice would be greatly appreciated.
 
updated 7.4 years ago • warrena
nbsp; mart = mart.snps)</code>
`` # returns 1 row ``
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86\_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5
locale:
\[1\] en\_US.UTF
updated 4.6 years ago • Marianna Foos
Dear all,
I have just installed the current R development version to verify whether my package works on the newest R release and I've encountered an issue when combining RangedData
updated 8.8 years ago • mdoering
Hi, I'm trying to get up and running to use openPrimer but am having some issues and would appreciate any guidance.
1. I get an error if I tag any primers as reverse. These go away if all primers are forward.
2. All melt temperature results using check_constraints are "NA".
3. Additional constraints throw new errors, but maybe because of #2? ... so one thing at a time.
# I believe I have depend…
updated 3.6 years ago • wnussbau
## Main Question
**What computational setups do you use for running EPIC array preprocessing pipelines?**
Specifically:
* Where do you run your pipeline?
- e.g. Personal PC, local network, HPC using scheduler like SLURM, etc.
* What configuration do you use?
- Nodes, cores, CPU, memory per CPU (or equivalent)
* What kinds of projects do you work on:
- Number of samples,…
updated 3.3 years ago • calen.p.ryan
<div class="preformatted">Hi
I am facing the following problem calling gcrma on an affy X. laevis
array. is there a quick solution or do i have to dig deep?
tia t.
> a
AffyBatch object
size of arrays=984x984 features (20 kb)
cdf=X_laevis_2 (32635 affyids)
number of samples=8
number of genes=32635
annotation=xlaevis2
notes=
> gcrma(a)
Adjusting for optical effect........Done.
…
gt; r
AffyBatch object
size of arrays=732x732 features (17 kb)
cdf=Drosophila_2 (18952 affyids)
number of samples=20
number of genes=18952
annotation=drosophila2
notes=
> eset_gcrma <- gcrma(r)
Adjusting for optical effect...a 'character'
Does somebody know why the conversion fails?
Regards,
Tobias
> sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu
loc…
ws,nit=10,nrit=1,empty_bins=TRUE,rank=FALSE)
Reading bam alignment Q97-k4_filter.bam
Total number of imported short reads: 13592073
Extending reads...
Creating GRange Object...
Extract unique regions...
Number of unique...be NA/NaN
Thank you very much!
thanks,
Yuting
-- output of sessionInfo():
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
l…
doesn't necessarily mean that there's
anything wrong with your linux installation, and
the limma versions for Windows and linux are
identical. There are differences in floating
point arithmetic between different hardward...in one
of the Lapack routines which apparently doesn't get tripped under
Windows.
You could try to identify which probe, or maybe
probes, is causing the error in linux and rem…
I tried to check the library, everything worked well
except the following error :
Problem number 1 :
'yeastAgilentLOCUSID' is deprecated
rather use 'yeastAgilentENTREZID'
see help("Deprecated")
In fact help("Deprecated...Quality control information for yeastAgilent
Date built: Created: Tue Aug 21 18:50:18 2007
Number of probes: 41419
Probe number missmatch: yeastAgilentALIAS;
yeastAgilentCHR…
updated 18.3 years ago • melany black
I have a question regarding underlying theory for significant probes and genes identified by a.) probe level differential methylation analysis using limma and b.) region level differential methylation...questions are as follows
1. **Why is there only around 12 percent overlap between significant CpGs identified at probe and region level**
2. (Likely will be answered by Q1) **Why are there only…
updated 7 months ago • jamiecatalano2
fullXmlQuery, :
The query to the BioMart webservice returned an invalid result.
The number of columns in the result table does not equal the number of attributes in the query.
Please report this on the support...site at http://support.bioconductor.org
sessionInfo( )
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.4
Matrix p…
updated 3.9 years ago • s.k.tepler
of R and Bioconductor:
1. On my Windoze laptop, I have R 2.6.2 and as far as I am aware, up
to
date versions of the relevant Bioconductor packages for 2.6.2. Doing
the GOstats works just fine.
2. On my Unix server, I have R 2.7.0...HyperGResultBase",
"hyperGTest")
1: hyperGTest(BPparams)
>
> sessionInfo()
R version 2.7.0 (2008-04-22)
x86_64-pc-linux-gnu
locale:
LC_CTYPE=en…
updated 17.5 years ago • Al Ivens
Also, depending on the size of your proteomics dataset (in terms of
how many proteins were identified by the mass-spec), you may
experience some instability in the results using the default number of
iterations. Try...running the plgem wrapper a few times one after the
other, and if you notice that the number of selected proteins is very
variable from run to run, then try increasing the number of…
updated 15.1 years ago • Pavelka, Norman
I understand that this question has popped up over and over again in this forum. The simple solution is to remove redundant categories to make rank full again. I would like to go further than this simple approach and figure out a conceptually more correct solution to this kind of problem.
Let me describe my experiment first: I have several strains of Strep. pneumoiae bacteria, with d…
Hi everyone,
I’m following section 4.7 in the using EdgeR user guide for differential methylation analysis using the count data associated with GSE86297 from GEO.
My output looks as it does in the user guide until I get to annotating CpG loci with the nearest gene. The command and output look like this:
```
>TSS <- nearestTSS(yall$genes$Chr, yall$genes$Locus, species="Mm…
updated 5.8 years ago • amlivernois
Dear All,
The reference manual for the development version of TRONCO (<https://www.bioconductor.org/packages/3.3/bioc/manuals/TRONCO/man/TRONCO.pdf>) disagrees with the actual
updated 9.6 years ago • Ramon Diaz-Uriarte
understanding of QSEA package. But I learnt from the tutorial and example dataset,
that QSEA identifies DMRs.Therefore, I think QSEA can compute sample-specific methylation values. I need help with the
function/command...and input data structure that can be used to identify sample-specific methylation values.
Any help is highly appreciated.
Thanks in advance.
Ann
updated 22 months ago • User3088
class="preformatted">Hi.
I am interested in plotting the chromosomal location of linkage
markers identified in genome screens of complex diseases with
differentially expressed genes that I have identified in microarray
updated 21.6 years ago • Anthony Bosco
each and every tissue but I am not sure how to go ahead with further analysis. My objective is to identify 1.identify modules in each tissue which are relevant. 2. a particular gene which is being expressed across all the...tissue. I am not sure on what basis should Identify the relevant modules of my interest .I do not have any clinical trait data that would help me shortlist a particular
updated 7.6 years ago • nazia
data that includes negatives. I am unable to perform the DESeqDataSetFromMatrix function to begin identifying differentially expressed genes. Is there a way to identify differentially expressed genes using log expressed
to use the R-devel branch to try to see if I
could overcome a problem I am having with the current version (1.8.6).
Actually 1.8.7 is the latest and fixes a bug that addresses your last
question below.
> I realized that my first...expect
it to be fairly unstable by then.
>>
>> Anyway, can you tell me which easyRNASeq version you are using (run
sessionInfo() or…
updated 11.7 years ago • Nicolas Delhomme
xout = xout, rule = 2) :
need at least two non-NA values to interpolate
I only have 140 DMPs identified for this data and makes me wonder if it is due to the low number of DMPs? Does anyone knows why this error occurs?
```r
DMR...annotated, lambda=1000, C=2, min.cpgs = 2) #C is an statistical factor, optimal at 2 #minimal number of CpGs that wou would consider to have a DMR defaul…
updated 20 months ago • Macsue
two groups but I'd be interested in
advice on how to analyse these data please. I am interested in
identifying differential changes in the resistant group which might be
leading to the acquired resistance. Would analysing...these data using
an ANOVA model be appropriate?
Thanks,
Dave
-- output of sessionInfo():
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale…
are several groups
represent
different disease subtype. I will just describe what I did here. I
identified significant genes. And extract the expression levels of
these
genes, and performed the cluster analysis using...Street
Room ZRC-527
New York, NY 10065
Phone 646-888-3220
huw@mskcc.org
[[alternative HTML version deleted]]
</div
I am trying to do a "classical" match of uniprot ids, using protein IDs identified in a Zebrafish mass-spec experiment, to find the corresponding ensembl gene ids. However, there are several proteins...ensembl_id gene_name
<0 rows> (or 0-length row.names)</pre>
<pre>
sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
loc…
central ID
used
by your annotation package.
For chip packages, this will still mean the central GENE identifier
used by
the package (NOT the probe IDs).
for creating the 'universeGeneIds' I used Entrez Ids from the whole
chip,
but...Biologe Moleculara
Universitatea Academiei de Stiinte din Moldova
[[alternative HTML version deleted]]
</div
updated 14.7 years ago • UnASM Lab_bi
extdata/single_sequences.2bit to write: No such file or directory
sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
updated 6.3 years ago • bioinagesh
with the parameters in order to perform a
more
stringent overlap - I would like to modify with the number of base
pairs
that need to overlap between coordinates in order for it to be
considered a
hit. I am unsure as to what mioverlap...Student
Johns Hopkins University/University of Southern California
[[alternative HTML version deleted]]
</div
updated 13.5 years ago • Kurinji Pandiyan
<div class="preformatted">Hello,
I am analyzing the GNF/Novartis data (Luscombe re-analysis
E-TABM-145). This experiment contains samples from a number of
organism parts. My aim is:
1. to compare the gene exprssions in a single organism part to the
average expression in all...the GNF/Novartis data (Luscombe re-analysis
E-TABM-145). This experiment contains samples from a number of
organism…
1: No package 'file29282' was found
in: packageDescription(p, lib = lib, fields = pkgFlds)
2: number of columns of result
not a multiple of vector length (arg 2) in: rbind(retval, c(p,
lib, desc))
Error: package 'reposTools' could...If not, what were the tricks?
Thanks,
Anton
[[alternative HTML version deleted]]</div
updated 20.6 years ago • Belooussov, Anton
<div class="preformatted">Hi,
I am new to microarray analysis with R and so have found the AffylmGUI
package a great help. I was wondering whether there is any way to
filter the
gene lists (as I guess you can with filterfun to weed out those genes
where
expression is too low on some arrays, etc and so reduce the number of
genes
that as being simultaneously tested) and then still benefit fr…
updated 20.6 years ago • Quentin Anstee
<div class="preformatted">Hello,
I have some HumanHT12v4 microarray data I am attempting to analyze
with
BioConductor. I ran processSwathData() on my data and receieved this
message:
>processSwathData(inputDir="123",outputDir="123",segmentHeight=397,seg
mentWidth=326,textstring="_perBeadFile.txt",verbose=TRUE,
twoColour = FALSE)
7964435065_A
Reading green locs1... green locs2... Do…
updated 12.2 years ago • Alan Hutchison
I am seeking to subset the GenomicMethylSet to the autosomes only.
Despite days of searching and a number of references saying this is
relatively straightforward, I have not yet had any success (have been
exploring GenomicRanges...direction with a code snippet or a reference?
Kind regards,
Toby.
[[alternative HTML version deleted]]
</div
updated 12.9 years ago • Toby Hughes
nuccore/62241012).
I'm now working using biomaRt and using the Ensembl accession
number ENST00000349310 as follows:
library('biomaRt')
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
getBM(attributes...the start of the cds with respect to the
transcript?
Thanks,
Andrew
[[alternative HTML version deleted]]
</div
intended or is it a bug?
<pre>
> library(rtracklayer)
> export(GRanges(), "test.gff", version = "3")
Error in data.frame(seqname, source, feature, start(object), end(object), :
arguments imply differing number of rows: 0...1</pre>
<pre>
> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.…
updated 8.8 years ago • jiri.hon
dans data.frame(Index = samps2$Index, `Sample ID` =
samps2$SampleID, :
arguments imply differing number of rows: 12, 0
De plus : Message d'avis :
In normalizeMethyLumiSet(mldat[, toKeep]) :
This function is probably not optimal for...some consequencies on the interpretation or the
result of QC ?
Greg
Montreal
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: x86_64-pc-mingw32/…
updated 15.1 years ago • gregory voisin
div class="preformatted">Dear Bioconductor users,
I am currently running the latest version of affy 1.4.22 under
R 1.9.0 on Mac OSX 10.3. I am able to get a boxplot on the
unnormalized
data
but not on the normalized...howard1.raw
AffyBatch object
size of arrays=640x640 features (67206 kb)
cdf=MG_U74Av2 (12488 affyids)
number of samples=21
number of genes=12488
annotation=mgu74av2
&a…
<div class="preformatted">Hi all,
I am doing some analyses of Affy arrays using limma. Following the
manual, I generated the fit2 object using the default eBayes settings,
and topTable with (almost) default settings.
> dim(eset)
Features Samples
22625 15
> fit <- lmFit(eset,designMATRIX)
> fit2 <- eBayes(contrasts.fit(fit,contrast.matrix))
&am…
gt; x
AffyBatch object
size of arrays=990x1190 features (20 kb)
cdf=MoGene-1_1-st-v1 (35556 affyids)
number of samples=9
number of genes=35556
annotation=mogene11stv1
notes=
Please notice that the "size of arrays" is wrong: x and...of "exprs(AffyBatch)", after loading the
.CEL-files, is also wrong.
Note that for the Gene ST version 1.0 arrays the above is not a
problem because the arrays are squ…
<div class="preformatted">Hi Eric,
Is CAGE the cap analysis of gene expression? Thanks!
I think the error has to do with the chromosome naming since there are
only chromosome X, 2L, 2R, 3L, 3R and 4 are available in drosophila
genome.
I am revising the ChIPpeakAnno paper which is due on Tuesday. Could I
get back to you after that? Thank so much!
Meanwhile, if others could help out, that…
updated 15.7 years ago • Julie Zhu
data using R / Bioconductor tools. The applicant will, in
consultation with other team members, identify appropriate analytic
approaches and work flows. The applicant will implement the analysis,
and arrive at scientifically...sound conclusions. The applicant will
identify common work flows, communicating these to other team members.
Secondary duties involve participation in ongoing...Experience…
Hello,
I have an RNASeq dataset containing 200 samples from asthma patients beginning therapy with one of two drugs (drug A and drug B), i.e:
Drug A: 50 samples pre-treatment (baseline)
Drug A: 50 samples one week post-treatment
Drug B: 50 samples pre-treatment (baseline)
Drug B: 50 samples one week post-treatment
I'm interested in using WGCNA to identify co-expressed gene modules i…
Hello,
I have successfully run edgeR on an ATAC-seq dataset to identify differential open chromatin peaks across two cell types. I wanted to normalise for peaks read count, GC content and peak width, so my method was to create a consensus peak set in Diffbind (2 cell types, 3 replicates per cell type), then to use the CQN package for normalisation steps. This creates a GLM offset to …
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