values for each
gene.
I wanted to know if I'm correct using
" N= RPKM x L x Ntot X 10-9
>where N = number of mapping reads at a given gene locus, L =
estimated length (bp) of the gene locus, Ntot = number of total
mapping reads, and...for differential expression analysis using DESeq?
Thank you,
Avinash
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</div
Order by: Relevance
gt; data
AffyBatch object
size of arrays=712x712 features (9 kb)
cdf=MOE430A (22690 affyids)
number of samples=12
number of genes=22690
annotation=moe430a
notes=
> ab <- Harshlight(data, na.sub = FALSE)
[1] "Generating Error...Images"
[1] "Initializing Harshlight"
[1] "Analyzing chip number 1"
[1] "Analyzing chip number 2"
[1] "Analyzing chip number 3"
[1] "Analyzing chip number 4"
…
updated 17.5 years ago • Guido Hooiveld
backticks as shown below
```r
BiocManager::install("DESeq2")
```
# Error: Bioconductor version cannot be validated; no internet connection? See #troubleshooting section in vignette# please also include the results...of running the following in an R session
sessionInfo( )
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (…
updated 2.5 years ago • Elham
Dear member of this group:
I got strange error when I update bioconductor to latest version 3.2, and I could not install GenomicRanges, IRanges packages. Here is the error what I ran into:
<pre>
> sessionInfo...R version 3.2.0 (2015-04-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 8 x64 (build 9200)
locale:
[1] LC_COLLATE...color:…
updated 9.9 years ago • Jurat Shahidin
is set to TURE if the peak start is inside the gene
(between gene start and gene end). Positive (+) number for
distancetoFeature
means the peak is inside or downstream of the gene. Negative (-)
number for
distancetoFeature...package, and have question about the
> "insideFeature". Could you tell me what "+" and "-" number
> (distancetoFeature) means? And how do you decide which peak…
updated 15.9 years ago • Julie Zhu
GOCat='BP', level=2)
switch level=2 to level=3 for GOCat='BP' it is working (indicating
different GO number)
but when I set up GOCat='CC' between level=2 and level=3 has the same
GO number
why the level has not effect on GO number when...La Jolla, CA 92037, USA
Phone 858-646-3100 ext. 3801
Fax 858-795-5298
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</div
updated 13.7 years ago • Zhi Zhang
div class="preformatted">Hi all,
I've been trying to retrieve SNP rsids using biomaRt for a number of
SNPs where I have their positions. My input file looks like this:
1 888899000 888899000
where,
1 = chromosome number...and the second and third numbers are the
position of the SNP.
My code looks like this:
library(biomaRt)
mart2 = useMart(biomart="snp", dataset="hsapiens_snp...because it'…
experimentData: use 'experimentData(object)'
Annotation: pd.mirna.4.0 </pre>
As far as I know, the number of probes of miRNA 4.0 is 36249, but the number of features of expression set generated after background correction...normalization, and summarisation was 36353. When I tried with affy package, the feature number was same as the probe number. 104 additional features were
&l…
updated 10.5 years ago • enthelesia
I am running DESeq2 package version : 1.30.0
I am doing a LRT on a data with 16K genes with 300 samples
On my Mac laptop the processing is fast. But the same...I am running DESeq2 package version : 1.30.0
I am doing a LRT on a data with 16K genes with 300 samples
On my Mac laptop the processing is fast. But the same code, same dataset, same package version of DESeq2 runs slow on a Linux serve…
updated 5.1 years ago • Saroop
using `` pvalRRHO() `` the resulting p-value is always `` 0 `` regardless of the lists I used or the number of permutations. The scatterplots on the other side make sense and the rho coefficient too.
Any help would be much appreciated...Best regards,
Aurelien
For info,
<pre>
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin14.5.0 (64-bit)
Running under: OS X 10.10.5 (Y…
within each replicate group."
Current language on the Cuffdiff site suggests that the current
version
of that program tests for whether the change is significant compared
to
changes in each condition.
http://cufflinks.cbcb.umd.edu
updated 13.9 years ago • Richard Friedman
<div class="preformatted">Job Title: Personalized Medicine Research Fellowship
Summary: Partners HealthCare and The Center for Biomedical
Informatics (CBMI), Harvard Medical School has one research fellowship
available for immediate appointment. The position is part of the
Partners Healthcare System - CBMI Program in Personalized Medicine
(PM)
whose mission is to identify and tra…
updated 17.4 years ago • Tonellato, Peter
openMP in order to greatly reduce some parts of
the
calculation.
We are proud to announce a new version of the software, rGADEM 2.0.
The code
is now up-to-date with the latest changes in the GADEM, the c version
of the
program...Wide Analysis of Transcription Factor Binding Sites from
ChIP-seq.
[[alternative HTML version deleted]]
</div
updated 14.4 years ago • Charles Joly
after which I have a data frame containing the following columns (9
columns and 5969 rows):
ORF (Identifier)
Name (Gene name (optional))
T1 - T7 (normalized log intensities for each of the 7 arrays)
Other then the above I have no...M. Kempenaar
Bioinformatics
Hanze University
Groningen, the Netherlands
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</div
updated 17.3 years ago • m_kempenaar@planet.nl
div class="preformatted">Hi all,
I have used the WGCNA framework to generate network and identify
modules.
Next, I wish to relate the modules with the disease status. My samples
include malaria parasites isolated...gmail.com
amit.subudhi@pilani.bits-pilani.ac.in
Mob No- 919983525845
[[alternative HTML version deleted]]
</div
<div class="preformatted"> Dear List,
I have been trying to use limma to identify differentially expressed
genes
but have been finding some difilcuties in creating a basic
model.matrix. and
establishing...div class="preformatted"> Dear List,
I have been trying to use limma to identify differentially expressed
genes
but have been finding some difilcuties in creating a basic
model.matrix…
div class="preformatted">Dear Michael,
We're interested in identifying CNVs from a single exome dataset (data
is Illumina paired-end, and there are no controls). Reading through
the document...mistake, please notify the sender
by return email as soon as possible.
[[alternative HTML version deleted]]
</div
being
passed
down to function 'plgem.write.summary'.
Both the developmental and the release versions of the package have
been updated and are now available for download from the Bioconductor
website.
The new version...numbers are as follows:
Bioc 2.6 release: plgem 1.20.1
Bioc 2.7 devel: plgem 1.21.1
To obtain the latest version, please follow
I am trying to use regionCount from gRanges on methylKit datasets and I get fewer rows than expected.
For instance I have a the CpG entries from mm10 in one dataset (geneC.obj) and the methylation counts in another (methC)
I only get 5 rows returned instead of what the equivalent of bedtools map -b methC -a geneC.obj which returns about 16010 entries
(after turning these data sets into bed file…
updated 21 months ago • Modoc Kesner
lt;- GenomicFeatures::promoters(txdb, upstream = 250, downstream = 0)
hha <- list(version="",
gff.features = txn, #all features in gff
genes = gene, #specifically CDS
promoters250 = pro250, #250bp upstream of any feature...reads = bam, peaks = peek, annotation = hha)
The output:
-----------
I haven't been able to identif…
updated 6.3 years ago • ryleehackley
We did our best to make these new packages look as much as possible
like
their environment-based version i.e. they can be used in the same way.
For the next release (BioC 2.2, April 2008) all our annotations will
be available...the old format
(environment-based). Hence you are highly encouraged to start using
the
SQLite-based versions as soon as possible.
Also we are providing much improved vers…
updated 18.2 years ago • Hervé Pagès
nucleotide sequence (25 mer) or its genomic coordinate
(chr & pos) as input and return exon number it maps to? Thanks a lot
for the help! Ying Chen
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</div
updated 13.5 years ago • ying chen
analyze illumina array
data. However, I have two sets of data that were obtained with
different chip versions and that have different number of probeIDs/
rows. Can I combine the two datasets (excluding the nuID's that are
not present
that simulates gwa-data for a quantitative
trait. I
would like to have a matrix with 0,1,2 for the number of minor allels
for
about 200000 snps (e.g. in columns) and the phenotypes (the
quantitative
trait) in rows.
Can anybody...give me a hint?
Thanks
Hermann
[[alternative HTML version deleted]]
</div
updated 12.3 years ago • Hermann Norpois
know your opinion/experience on the fastest (and
memory
parsimonious) way in BioC for counting the number of reads for each
region.
Thanks!
mattia
[[alternative HTML version deleted]]
</div
updated 12.9 years ago • mattia pelizzola
In some cases, we should clean the paired end data. and then
the processed data have not same number in paired end data.
how to check them id and delete those only appearing in one
end
data.
thx
shan gao
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</div
updated 14.2 years ago • wang peter
generated from SNP
data).
Although the LD from SNP data is relatively straight forward through a
number of the R libraries.
Thanks very much
[[alternative HTML version deleted]]
</div
memory problems.
Does
somebody have an idea of the requirements of a PC able to analyze such
a
number of chips?
Thank you
Simona
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</div
updated 17.5 years ago • simona dalle carbonare
Positive Control</pre>
However, there seems to be a problem with the current version of the pd.hta.2.0 package (version 3.12.1) because when I use affycoretools::getMainProbes(), the only available annotation...support.bioconductor.org/p/86207/\#93117, written 5 months ago), that there will be an updated version of the pd.hta.2.0 package (version 3.12.2) where this is fixed and I wondered …
updated 8.4 years ago • relathman
TFB"), maxgap = 0, totalTest= 10000, cex = 1,
counts.col = "purple")
totalTest specifies the total number of tests performed to obtain the
list of peaks. This number should be larger than the largest number
of peaks in A and...function depends on how totalTest is
defined, but shouldn't it be defined by the peak number of TFB? The
larger I make n (by increasing my totalTest number) in the funct…
updated 15.4 years ago • Noah Dowell
to use cghMCR to find common regions in 32 samples
(244K
mouse agilent array)
I have installed version 1.8.0
I have done this first step sucessfully
require("limma")
arrayFiles <- list.files(system.file("Data", package...Trust Sanger Institute is operated by Genome Research
Limited, a charity registered in England with number 1021457 and a
company registered in England with number 2742…
<div class="preformatted">Hi Pan,
I have 2 lumiBatch objects, both with controlData slots, filled in via
addControlData2lumi.
When I combine these 2 objects, the controlData was silently not
combined. This is because my controlData slots had different numbers
of rows.
Could you please provide a warning within setMethod("combine",
signature("LumiBatch","LumiBatch"), ...) if the nrow controlD…
qseaSet, uniquePos=TRUE, paired=TRUE)
but I keep on getting the error below.
I am running version sea\_1.6.0 and running on a custom BSGenome reference. Any suggestions are greatly appreciated.
Madi
Reading...bam alignment combined_bams/S4_Apo1_ALL_sorted.bam
Number of imported sequencing fragments: 13908900
Calculating short read coverage for genome …
updated 7.6 years ago • apt.university
this something we are not supposed to do)?
I created my large MethylSet object under the pervious version of R
and
Bioc and at the time the annotation package
IlluminaHumanMethylation450kannotation.ilmn.v1.2 was...MethylSet preprocesses as 'Illumina,
bg.correct
= TRUE, normalize = controls, reference = 1'
minfi version: 1.8.1
Manifest version: 0.4.0
>
> class(mset)
[1] "Methyl…
updated 12.2 years ago • Florence Cavalli
profiling using
RNA-Seq, ChIP-seq analysis of DNA-bound proteins, and cancer genome
re-sequencing to identify SNPs, indels, copy number aberrations and
structural variants. Encouragement and support will be provided to
develop...with the ability to work well in a
team.
http://www.cruk.cam.ac.uk/
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</div
updated 11.4 years ago • Suraj Menon
<div class="preformatted">Dear list,
I have a mosquito microarray that I would like to annotate, but am
having
some trouble figuring out which packages are appropriate to use.
After
reading the Annbuilder, Annotate and BiomaRt vignettes, I am still
really
unsure if any of those packages would do what I want. So here is my
question:
The array is for Anopheles gambiae, and consists of abou…
updated 19.8 years ago • Amy Mikhail
<div class="preformatted">Hi Allen,
The GOID should include "GO:" before the numeric number.
> library(lumi)
> library(lumiHumanAll.db)
> m <- mget("GO:0043473",lumiHumanAllGO2PROBE,ifnotfound = NA)
> m
The returns are corresponding Illumina probes (identified by nuIDs)
included
in all types of Illumina Human chips. If you want to know the original
Illu…
update_date
<0 rows> (or 0-length row.names)
It seems, for starters, that this GDS identifier for my particular
submission isn't accounted for in the current
database.
Others are, so it looks like my syntax...GDS17
8 GDS18
9 GDS19
10 GDS20
There is also the question of where a set of fields (variable in
number) describing sample factors and their levels would actually
"live"
in…
class="preformatted">Hi Valentina,
Well it's not all that surprising, because 6666 is a much bigger
number
than 0! What you mean of course, is that the large count 6666
represents
some sort of outlier process that you don't want...empirical Bayes
procedure
into edgeR and limma that I think you will find far more effective.
It
identifies outlier genes with very high variances while maintainin…
tables of (m/z + retention time vs. samples), which I generated using XCMS online. My goal now is to identify differentially abundant peaks, as one does with gene expression for RNA.
I filtered features for a given table as...direct interest but could contribute to variability as a column in the design matrix.
In terms of identifying differentially abundant peaks, I followed [Gordon’s advi…
updated 2.9 years ago • wiscoyogi
<div class="preformatted">
Hello all,
I have a cDNA array data sets collected from a time-course experiment.
The
experiment design was similar to the following:
1)Treat cells with ligands A, ligand B, or a vector control
2)Harvest cells at 1h and 2h
3)Measure expression changes in treated cells relative to
time-matched-controls using 2-color cDNA arrays with a dyeSwap design
(each
treat…
exons...OK
Processing chromosomes...Fetch seqlengths from ensembl, dataset hsapiens_gene_ensembl version 74...OK
OK
Generating index...OK
-------------
Verifying validity of the information in the database:
Checking transcripts...OK
Checking
updated 9.6 years ago • stianlagstad
message when I attempt to convert a GRanges value to a RangesList. This never happened in the older versions. Does anyone know a way around this? I'm using known human polyA sites. Here is a quick snippet of the code I've been using
updated 7.5 years ago • hicklingmeb
div class="preformatted">Dear BioC
I would like to use biomaRt to get entrez gene (or other) identifiers
for small tag sequences. I use the getFeature function for this. It
seems that it will retrieve the identifiers...8",
start
= "13550741", end = "13550761",mart=ensembl)
sessionInfo()
----------------------
R version 2.5.0 (2007-04-23)
i386-pc-mingw32
locale:
LC_COLLATE=English_United Sta…
Hello,
I'm running "identify" function as idx <- identify(resLFC$baseMean, resLFC$log2FoldChange). I think it would be quite fast, but it's taking...forever. Is it ok to run "identify" after "lfcShrink(dds, coef = "xx", method = "apeglm)" ?
Thanks,
Luciana
updated 6.8 years ago • lucianalpt
dba.report don’t work in my DiffBind 2.2.12. I guess that it is because my DiffBind is not the last version, i.e. 2.4.8. However, when I install DiffBind again, it is still the 2.2.12 version. Could you help me and please see the...gt; source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
A new version of Bioconduct…
updated 8.3 years ago • Gary
data has 1
The code worked a couple of weeks ago. I guess that there is a bug in
the latest edgeR version that is causing this? Interestingly, I cannot
reproduce the error using the example data in the DGEList manual:
y <...y, group=rep(1:2,each=2))
I would be grateful for any help!
Cheers,
Katja
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64…
The latest version of RSQLite (on CRAN) broke my package, [DECIPHER](https://bioconductor.org/packages/3.8/bioc/html/DECIPHER.html), in both...have the minimal set of git commands to sync the release branch with devel, while updating the version number in release? Any assistance would be much appreciated. Apologies in advance that I am not a git wizard
updated 7.6 years ago • Erik Wright
<div class="preformatted">Dear Bioconductors,
I have some proteomics data for several tissues:
Heart x 3 replicates
Lung x 3 replicates
Each data set has a gene symbol and the number of peptides for that
gene (a
rough measure of protein expression).
I want to make a data structure like:
heart1 heart2 heart3...several tissues:
Heart x 3 replicates
Lung x 3 replicates
Eac…
updated 15.8 years ago • Johnny H
div class="preformatted">Matt,
Many thanks for helping us identifying the bug introduced in 2.12.2!
The bug has been fixed in version 2.13.1. Please let me know if you
have any issues...S -FS" <mszinkgraf at="" fs.fed.us=""> wrote:
Hello Julie
I recently updated ChIPpeakAnno from version 2.10 to 2.12.2 and I am
getting incorrect results from annotatePeakInBatch.
More specifically the o…
updated 11.4 years ago • Julie Zhu
data with different samples size. For example(10 methylation samples,15 gene expression samples).
I identified DMRs using bump hunter in minfi package. I want to integrate gene expression and methylation data using DMRs...identified using bump hunter.
I found bioconductor packages that can do integration for methylation and gene expression...like MethylMix and methylAnalysis but both packages d…
updated 9.4 years ago • Asma rabe
in DESEQ2 using default parameters. However, if i input the same count matrix to the latest deseq2 version i don't get the same normalized values. Moreover, if i use the vst transformation in deseq i get values different from...my deseq2 run and my friends run. So the calculations evolved over time I guess. I do admit the numbers are close but not exactly the same which i need for reproduction. W…
updated 8.3 years ago • aa1201
latest CellRanger software 3.0.2. I was unable to load the molecule_info.h5 file with the released version of DropletUtils. I was told that I needed to use the development version of DropletUtils for newer cellranger output...So I installed a development version of R to then install the development version of Bioconductor and then the development version of DropletUtils. I...am using the devel…
updated 6.7 years ago • Matthew Thornton
Dear list,
I am trying to analyze a set of affy human 500k mapping snp arrays. I
try to make copy number calls and relate them to candidate genes.
I am wondering: what is the most popular package for such a task?
Thank you.
Xiaokuan...alternative HTML version deleted]]
</div
div class="preformatted">Is it possible to query BiomaRt and get the number of binding sites of
a miRNA with a target gene ?
I believe the coordinates of each binding site can be extracted as
well...such information, if any ?
Thank you.
Maura
tutti i telefonini TIM!
[[alternative HTML version deleted]]
</div
B) it was called DEG even though it was only detected in one sample.
For (A & C) these were NOT identified as a DEG with DESeq2 but were identified with edgeR's glmQLfit().
For DESeq2 I ran this with the default parameters...algorithm itself. I can also provide more examples if that would be helpful.
Thank you!
![NOT identified as a DEG with DESeq2 but was identified with edgeR'…
updated 4.8 years ago • lnblock2
Hi Erik,
I have the following issues with the design probe function:
> probes <- DesignProbes(tiles, identifier="Streptococcus",start=120, end=1450, batchSize=100,numProbeSets=5)
StreptococcusWarning message:
In DesignProbes(tiles, identifier = "Streptococcus", start = 120, :
No target sites met the specified constraints: Streptococcus
>probes <- Design…
Hi there,
I'm working with some RNASeq data to try and identify any differential gene expression (DGE) between disease states in edgeR.
Disease can be one of three levels: No Disease...of the latter two levels). Depending on how I set up the contrast, I get wildly different numbers of DGE.
My understanding of contrasts was that the absolute values do not matter so long as they work out …
Dear all,
I have 450k methylation data from 120 samples. I perform differential methylation analysis (using the m-values) for a interval scaled variable (current\_phenotype with levels of 1,2,3) with limma which identifies 1336 hypo- and 635 hypermethylated CpG´s.The significant CpG´s (FDR<0.05 & logFC > 2) are then used for an analysis of differentially methylated pathways…
updated 9.8 years ago • philipp24
<div class="preformatted">Hi,
I am reporting a biomaRt error noted during some work. The code did
not return the flanking sequences of a SNP.
> getBM(attributes=c('refsnp_id', 'chr_name', 'chrom_start', 'allele',
'c57bl_6j', 'cast_eij', 'upstream_flank','downstream_flank'),
filters=c("snp_filter"), values=( "rs6171921" ), mart = snpmart)->sps
Variation Name Chromosome nam…
Recent ...
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