I have been working on a large scale RNA-seq data analysis that are generated over 5 years. We don't have control genes and our phenotypes are continuous variables. We are trying to find the unwanted variables without depending on any phenotypes or control samples/genes. We have tried clustering/PCA. The clusters were not clear to us. Welcome any suggestions! Thank you very much!
Tongjun
Order by: Relevance
Hi community,
I used sva on DESeq2 normalized count.
>mod=model.matrix(~group, colData(dds))
>mod0=model.matrix(~1, colData(dds))
> sv=svaseq(counts(dds, normalized=TRUE), mod, mod0)
Is it recommended to use these SVs in removeBatchEffect(), and how should it be done if it is recommended?
Thanks.
updated 23 months ago • Xiao
Hi everyone,
I´ve built a SOM tree using FlowSOM with a normal bone marrow sample. In order to understand the map, I would like to gate populations manually and then check the position of those populations within the SOM tree. Is that possible?
![SOM tree obtained from FlowSOM][1]
[1]: /media/images/09557c1d-822f-48a4-8b68-bb368855
updated 2.1 years ago • agus_rizzo
Dear All,
I am using EdgeR package to extract the differential expression . I do not have replicates in my samples.
Now I want to know the normalized read count of my datasets.
I have tried with rpkm method but edgeR follow the TMM method for normalization so there is a variation at normalized read.
Could anyone suggest how can I get the normalized read count for all my reads.
Here is my cod…
updated 7.4 years ago • shuklashweta33
Hi,
I'm looking for a package that will give me the sequence of affy
probes in the Human?U133A 2.0 package. In other words, I have a list
of affy ids (e.g. 237488_s_at, etc.) and I would like to know the
sequences of original 25 mers this probe corresponds to.
Thanks,
Schragi
Hi,
nice to meet to you,
now i am planning to convert ENSG id into Gene Symbol based.
would you tell me how to do it ?
regards, thanks in advance !
updated 9.4 years ago • maedakus
hi,
I was wondering how dexseq is calculating the differential exon usage. I am having troubles interpreting the results, which I think are significant, but dexseq does not :-)
I have here one of the genes from my run, which looks to me, that it is very much differentially used. the three plots are the results for the counts, the expression and the splicing events calculated by DEXSeq.&nb…
updated 8.8 years ago • Assa Yeroslaviz
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updated 18.5 years ago • Guido Hooiveld
Dear all,
I'm doing gene expression comparisons between two groups of subjects
using affymetrix single-channel hgu133plus2 microarray chips and I
have
two questions.
1) Relationship among manufacturer ID, EntrezID, GenBank ID and gene
SYMBOL: Is there any one-to-one mapping?
I noticed that the hgu133plus2 environment gives annotations through
Entrez ID. Is this always the case? It seems to me …
updated 18.3 years ago • Chunyan Liu
Hello there, I am using Windows 10 machine. Trying to get GEO files using getGEO function. Since the internet is sporadic in my part of the world, I always try to download files separately and call it through R-console. But I couldn't get the GEO files using `` getGEO() `` function. I searched the support website and found to directly link the soft file.
> getGEO("GPL6480.soft")
# Error …
I need help on how to cremove control probes from Affymetrix Human Gene 1.0 ST Array probe set version?
This is what I use for the code, however, I think this is only applicable in some affy chips.
```cont_MZL <- grep("AFFX", rownames
updated 17 months ago • drexjaramel
please also include the results of running the following in an R session
sessionInfo( )
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS 15.6.1
Matrix products: default
BLAS: /System...Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4...x86_64/Resources…
updated 9 weeks ago • yoav.lubelsky
dds <- estimateSizeFactors(dds)
> dds <- estimateDispersions(dds)
sessionInfo( )
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS...For context, I am using these dispersion estimates as input for running ImpulseDE2 to identify time-dependent genes using time series RNA-seq data wi…
updated 4.6 years ago • rohitghosh
<div class="preformatted">Job Title: Personalized Medicine Research Fellowship
Summary: The Center for Biomedical Informatics (CBMI), Harvard
Medical School has one research fellowship available for immediate
appointment. The position is part of the Laboratory for Personalized
Medicine (LPM, lpm.hms.harvard.edu) program to reengineer
translational science and accelerate the migration of b…
updated 12.3 years ago • Doe, Aimee
<div class="preformatted">
All,
I am a new edgeR user. I have difficulty understanding the meaning of
the ???cpm??? function of edgeR package. I mean I understand that
each value is divided by the total library value, and then multiplied
by 1,000,000. But why 1M? I don???t understand what is the logic
behind using 1M? is it 1M reads? Or bases? And why not 10M? or 1000?
Any specific reason…
of development. The "trait" data is just the developmental stage. So I have a trait file with "Stage" (numbered 0-5) and "Individual". I added X's before the individual names in both files, because they were just numbers. When I try and...where the row names are...
Any help would be appreciated! Thank you!
> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86\_64-apple…
exp1.all.raw
AffyBatch object
size of arrays=712x712 features (47532 kb)
cdf=MOE430A (22690 affyids)
number of samples=12
number of genes=22690
annotation=moe430a
> sessionInfo()
R version 2.1.1, 2005-06-20, i386-pc-mingw32
attached
updated 20.4 years ago • Dick Beyer
<div class="preformatted">Hello List,
I'm just starting with R and wanted to analyze my data for
differential
expression using edgeR. Here is the code which is working for me but I
want
to check if I'm missing something as I get more number of
differentially
expressed genes compared to DESeq
MY Sample data
GeneID CR1 CR2 MR1 MR2
3119s00200.1 78 78 148 124...Here is the code which …
Failed to perform HTTP request.
Caused by error in curl::curl_fetch_memory():
URL rejected: Port number was not a decimal number between 0 and 65535
---
Backtrace:
1. global getMart(...)
2. base::tryCatch(...)
3. base (local) tryCatchList(expr...expr, names, parentenv, handlers[[1 L]])
14. value[[3 L]](cond)
sessionInfo( )
R version 4.4.1 (2024-06-14)
Platform: aar…
updated 14 months ago • Abiologist
Desktop/08272014/IDATs")
As confirmation that all of the features were imported, I checked the number of rows in methyLumiSet:
<pre>
nrow(methyLumiSet)
Features
485577</pre>
The methyLumiSet is based off of the eSet class...lt;- methyLumiSet[fData(methyLumiSet)$CHROMOSOME=="Y", ]</pre>
however, when I check the number of probes, the result is 0 features:
<pre>
…
updated 10.5 years ago • martens.christopher
gt; abatch
AffyBatch object
size of arrays=1002x1002 features (8 kb)
cdf=Mouse430_2 (45101 affyids)
number of samples=4
number of genes=45101
annotation=mouse4302
notes=
> tmp <- new ("ExpressionSet", phenoData = phenoData(abatch...sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b
varLabels and varMetadata:
sample: arbitrary numbering
pheno1: arbitrary numbering
featureData
ro…
updated 18.3 years ago • Min Wook Kim
to find ensemble gene ids for the 1372 mouse entrez gene
ids via biomaRt.
but I find different number of genes in result when I do it with
biomaRt package compared to BiomaRt online tool.
Strangely online tool gives atleast...updated?
Konika Chawla
PhD candidate
Department of Biology
NTNU
[[alternative HTML version deleted]]
</div
function to the sampleNames function, as shown below:
> sampleNames(affydata);
The number, order and string values returned by both statements should
match.
Manuel X. Duval, PhD
University of New Haven
Biology...Adjunct
Biological Sciences
mduval@newhaven.edu
Cell: 860-287-3570
[[alternative HTML version deleted]]
</div
updated 12.5 years ago • Duval, Manuel
phenoData object with 2 variables and 17 cases
varLabels
sample: arbitrary numbering
Subsetting for status:
1) test<-eset[,eset$status=="C"] gives me
Error in validObject(.Object) : Invalid "phenoData" object...work fine with the
Biobase eset, but not with my exprsSet.
Thanks,
Beth
[[alternative HTML version deleted]]</div
<div class="preformatted">This is an automated message sent out weekly to report recent changes
to Bioconductor packages. Please see the URL
http://www.bioconductor.org/changelog.html for a complete history of
changes. Unless otherwise noted, these changes apply to the
developmental
packages only.
----------------------------------------------------------------------
-
Oct. 31 2003: metaD…
updated 22.0 years ago • madman@jimmy.harvard.edu
o Preto
*Universidade de São Paulo
--
No trees were killed to send this message, but a large number of
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were terribly inconvenienced.
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</div
updated 12.4 years ago • Simon Coetzee
<div class="preformatted">As part of a ?6 million investment in its research portfolio the
University
of Birmingham is launching a programme of prestigious Research
Fellowships.
The fellowships will last for five years and, subject to normal
probationary
procedures, will lead to permanent academic positions. All successful
candidates will be required to perform some teaching in the last thr…
updated 21.5 years ago • Wei, Wenbin
fit, cont.matrix)
> fit2 <- eBayes(fit2)
> s24vss0<-topTable(fit2,coef="s24vss0",number=400,adjust.method="BH",
p.value=1)
>
> write.table(s24vss0,file="s24vss0.txt",sep="\t")
>
>
> s48vss24<-topTable(fit2...coef="s96vss48",number=400,adjust.method="BH
",p.value=1)
>
> write.table(s96vss48,file="s96vss48.txt",sep=…
<div class="preformatted">Hello,
Last week I was sent GenePix data files from an associate. As far as
I'm aware, these files have not been edited in any way before being
sent
to me.
My aim was to load them up and run some marray and/or limma functions
on the data.
First I tried to load the files (16 of them) using read.GenePix(), but
this failed with an error:
Error in "colnames&…
but I cannot complete the vignette with the data provided. Perhaps I am accessing an outdated version?
When I first load the p dataset, I am missing some information. I would appreciate being pointed in the right direction...my console:
<pre>
> library("Pbase")
> data(p)
> p
S4 class type : Proteins
Class version : 0.1
Created …
updated 10.3 years ago • nic.bowman
sample names<= tmp value = c (sample 1 sample 2 sample 3)
value length (8) must equal sample number in assay data (0).
I have a question for lumi developers, were there changes in the most
recent version of the lumi package...isn't
necessary (in the case when this is a known change in behavior).
Here's the sessionInfo():
R version 2.9.2 (2009-08-24)
i386-pc-mingw32
locale:
LC_COLLA…
Dear All,
I am analysing a gene expression profiling (Illumina microarray) of 12 samples, 6 of them are organoids and 6 are the matched tumor samples. The gene expression profiles of organoids and tumor samples look different and I identified hundreds of genes differentially expressed (lmfit+eBayes+topTable, adj-p-value < 0.05). The goal of my project is...tumor samples. The gene expressi…
updated 9.0 years ago • Keifa
Hello,
I would like to use DESeq2 to identify peaks in ChIP-seq or CLIP-seq for given regions. As I have specific regions, I want to use DESeq2 instead of peak caller...Specifically, I have a read counts table for input and IP(pulldown) and want to compare them to identify enriched regions. In the case, can I use default DESeq2 pipeline similar as DiffBind ? Or Do I need to use one-sided test
<div class="preformatted">Hi,
I'm comparing the response of two viral strains to their host
environments over a timecourse. Viral RNA abundance is measured at 0,
0.5, 1, 2, 4, 6, 18 and 24 hours post-infection. I am looking for
procedures that will identify viral homologues in the two strains that
show differential expression. For example, consider gene A1 in strain
1...at 0,
0.5, 1, 2, 4, …
updated 16.6 years ago • Anjan Purkayastha
AffyBatch object
size of arrays=744x744 features (17 kb)
cdf=HT_HG-U133A (22277 affyids)
number of samples=3
number of genes=22277
annotation=hthgu133a
------------------------------------------
I tried to solve this problem by all means:
changing the qc environment...setQCEnvironment("hthgu133acdf");
remove the "hthgu133acdf" package, then reinstall it;
updating the version of R from 2.10 to 2.…
updated 14.2 years ago • Guest User
I've tried to duplicate this with 2.1.3 from
the
devel library and the current release version and it works fine for me
on windows and on linux. Please can you try updating to 2.1.3 and
seeing
if that fixes things...gt; all.raw
AffyBatch object
size of arrays=712x712 features (11889 kb) cdf=Zebrafish (15617
affyids)
number of samples=3 number of genes=15617 annotation=zebrafish
> all.mas5…
updated 20.4 years ago • Crispin Miller
where = topenv(parent.frame())) :
"AffyGenePDInfoPkgSeed" is not a defined class
Enter a frame number, or 0 to exit
1: new("AffyGenePDInfoPkgSeed", author = "authorname", email =
"mwkimpel@gmail
2: getClass(Class, where = topenv(parent.frame...calls[1:from])
repeat {
which <- menu(calls, title = "\nEnter a frame number, or 0
to
exit ")
if (which >…
**Summary**
It seems featureCounts under certain circumstances ignores the ```isPairedEnd = TRUE``` argument.
**Background**
I have been using featureCounts successfully for many years but recently ran into a problem in files where I have a mixture of paired and unpaired strand specific data (Produced by Trimmomatic mapped by Hisat2 (v 2.0.1-beta)). To illustrate the problem consider t…
updated 6.6 years ago • k.vitting.seerup
<div class="preformatted">Dear list,
I would appreciate if someone can clarify for me this - seemingly -
simple issue:
I have probes for the probe set:
probes1 <- subset(drosophila2probe, Probe.Set.Name == "1631333_s_at")
> as.data.frame(probes1)
sequence x y Probe.Set.Name
Probe.Interrogation.Position Target.Strandedness
119715 CTCACATTCTTCTCCTAA…
I have run a first analysis using Limma and made pairwise contrasts. I
have found that the number of differentially expressed genes increases
as I compare diets with larger differences in concentration of the...eBayes(fit1)
topTable(fit2,coef=2)
that suggests to simply change the value of the factors to a number.
However, if I try to adapt it to my case:
var1 <- c(0, 12.66, 25.32, 37.98,…
updated 12.2 years ago • Christian De Santis
I am using xcms for metabolomic work, and I'm coming across a bug that I can not seem to track down. I've scoured the online forums and am trying a grid search of various parameters, but I'd love to get your input on this problem.
__My Goal:__
To identify features in an experiment with various samples that are independently injected into the mass spec and correct for retention time.&a…
myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author
=
list(author = "Julien TEXTORIS", maintainer = "Julien.Textoris at
gmail.com"),
fromWeb = TRUE...myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir,
organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, author
=
list(author = "Ju…
updated 19.9 years ago • TEXTORIS Julien
per group. When performing QC plotting, I find that PCA and clustering of vst-transformed values identifies some samples as quite different from the others:
<pre>
# Read dds
dds <- readRDS(dds.path)
# Variance stabilizing transformation...mainly the differentially expressed genes.
Thank you!
Best,
Joe
<pre>
> sessionInfo()
R version 3.5.1 (2018-07-02)
Pl…
updated 7.3 years ago • ipso
executed on same count files. Apart from base mean, all other columns have different statistical numbers for every row.
Perplexing thing is that normalized counts are same for both the runs but pValues and log fold change...differently from the earlier run is that I had to reinstall DESeq2. I do not remember the previous version that was installed. Can this be related to differences in the pa…
updated 22 months ago • Kuldeep
this have been documented? I didn't think this
type of change would have been included in a
minor version upgrade. What was the explanation for the original
discrepancy?
Thanks,
Jenny
#The examples below are not reproducible...gt; raw
AffyBatch object
size of arrays=834x834 features (10 kb)
cdf=Rat230_2 (31099 affyids)
number of samples=6
number of genes=31099
annotation=rat2302
notes=
>…
BioC 3.8.
How can I run the ssdCoverage command, originally found in htSeqTools, using the latest version of R and Bioconductor? Are there alternative methods that are not deprecated
updated 4.7 years ago • Mick
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updated 20.1 years ago • Stan Smiley
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updated 18.5 years ago • De Bondt, An-7114 [PRDBE]
I'm using `` viewApply `` to apply a function on each element of a `` SimpleRleViewsList ``. The function is rather slow, so I was wondering whether there was a way to execute `` viewApply `` in parallel (or something similar)?
updated 8.6 years ago • maltethodberg
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updated 18.8 years ago • Karen Vranizan
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updated 18.4 years ago • el mousselly antra
Dear all,
I and some collegues still use R 2.14 on my machine.
The current update of mzR gives a warning that it was built
for R 2.15 and later crashes if loaded.
I'm not an experienced R user, so my question:
Is there a way to supress such "dangerous" updates ?
I know that updating R should circumvent this problem,
but this requires admin rights, which I can not assume
in general.
Kind Regar…
Since the multicore architecture has become very basic to almost all
types of personal computers and powerful enough to do the same jobs as
cluster architecture, in particular, there are a couple of R Packages
that have provided parallel computing for both cluster and multicore
architectures, I wonder whether there is any future development for
Maanova to use multicore machine for parallel compu…
I am having troubles using simpleaffy as follow :
I am writing <raw.data <-read.affy("covdesc")>
and getting this error:
>Error in read.affy("covdesc") : could not find function "read.affy"
I have bioconductor and downloaded all required packaeges and yet having this error with no explanation
any help is highly appreciated
updated 8.0 years ago • amaalkalds
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updated 20.3 years ago • A.J. Rossini
org.Hs.eg.db)
>
> query.cnv <- GDCquery(project = "TCGA-LUAD", data.category = "Copy Number Variation", data.type = "Gene Level Copy Number",platform="Affymetrix SNP 6.0",legacy=FALSE)
--------------------------------------
o GDCquery: Searching in GDC...for the query
-------------------
o Preparing output
-------------------
> sessionInfo()
R version 4.1.1 …
updated 4.1 years ago • raf4
in
Pfizer, and it runs quite fast (< 1 hr) for 1000-iterations.
LPE is best suited if the number of replicates and samples are less
than or equal to 5. We upgraded the LPE package from the original
paper (2003), and published...a paper in BMC Bioinformatics. The latest
version is on Bioconductor since early last year.
(http://www.biomedcentral.com/1471-2105/6/187)
Originally, when we col…
div class="preformatted">Hi all,
??? We are using two methods to identify SNPs. One is based on
resequencing the genome and aligning the reads to the sequenced genome
to identify SNPs (data
to the field, and I'm trying to do a differential gene expression on the GTex dataset. My aim is to identify sets of genes which (with some confidence) identify each of the 50 odd tissue types in the said dataset. The dataset
i2xy, xy2i
AffyBatch object
size of arrays=640x640 features (27212 kb)
cdf=HG_U95Av2 (12625 affyids)
number of samples=4
number of genes=12625
annotation=hgu95av2
notes=
Now, following the vignette I try,
> image(Dilution)
Error...2.8.
I look forward to hear from some of you.
Thanks in advance,
Omar
[[alternative HTML version deleted]]
</div
updated 14.6 years ago • Omar Gutierrez Arenas
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