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updated 2.6 years ago • sonachinarayan
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updated 2.6 years ago • sonachinarayan
<div class="preformatted">Thx for the help...
mdiv <- function(dec)
{
dec <- dec * 4
dec <- round(dec, 0)
dec <- dec / 4
dec
}
where m is a matrix --
m1 <- apply(m, 1, mdiv)
...but it looks like as.integer(x.1*4)/4 or (round(x.1*4,0))/4 might
be
easier...
thx again,
ken
>From: james.holtman@convergys.com
>…
updated 20.5 years ago • Ken Termiso
I would like to simulate a dataset with two distinct groups of cells, and with the desired amount of DE genes if possible. In my case, I just want to test a method whether its performance is sensitive with a series of the increasing number of DE genes. For example, I would like to simulate a dataset of 500 cells and 5000 genes which has only two groups, with 150...I just want to test a method w…
<div class="preformatted">Hi
I have a microarray data comprised of 3 treatment conditions (N,M,I)
and
2 time points (4dpi and 5dpi).
I used limma - ebayes fit and toptable with coefficient for a specific
contrast to get the differentially expressed genes and adjusted P
value.
I also did a ANOVA test, and I want to know which one is better to
identify differentially expressed genes.
CODE: f…
updated 11.4 years ago • Konika Chawla
am unsure how to go about doing the design and contrasts for 5) and 6). Essentially I would like to identify genes showing different patterns between GFP and GeneA in HSC vs HLFs in limma (i.e. increasing in HSCs and decreasing
updated 4.3 years ago • sam41251
I need to install the latest version of S4Vectors in order for the affycoretools package to work. I tried to use the latest installation instructions...on the Bioconductor website, but when I check the version of S4Vectors it still shows 0.26.1 rather than the latest version 0.27.12. I install and use the 'devel' package as per
updated 5.3 years ago • ianrector97
div class="preformatted">Hi, BioC Members,
I have a general question on identifying DE genes. Since there are
many ways
to do this, I am wondering whether people has compared methods such as
SAM,
EBAM...they always
give
similar results (assuming the parameter settings are optimized to get
similar number of DE genes)? Is it better to get a common list of
genes
using three different methods? Do…
do some basic visualisation on it through the oligo library, I can also create heatplots of the top \# number of results (though not accounting for multiple testing) (trying to run it on full array resulted in R uing over 15GB of...contains no useful data (see structure pasted below, hopefully I got my formatting right)
R identifies the arrays as `` pd.mogene.2.0.st ``
So my question is what am…
updated 5.0 years ago • ben_cossins
it easy, I have written a simple R function to install all required packages (see below with limited number of packages for the example).
install\_packages <- function(){
\# Open R and install packages
 ...problematic, giving me error messages of this kind:
package ‘edgeR’ is not available (for R version 3.1.2…
<div class="preformatted">Dear List,
I am trying to download some annotation information from using biomaRt
package.
I am using some ENSG gene Ids as an identifier and trying to download
more annotation
information about those ENSG gene Ids from archived version (ENSM 50).
what I do here is download two different data frames with different
attribute sets.
For some reason they have differen…
updated 15.1 years ago • Md.Mamunur Rashid
div class="preformatted">
Hi,
I installed the latest version of R and tried to install the
compatible Bioconductor version but get the following error message:
source("http://bioconductor.org...biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.1), ?biocLite for help
> biocLite()
Error: 'no packages in repository (no internet connection...bioc
Does anyone have a solution for …
updated 11.6 years ago • Guest User
I cant reproduce results that I got
before. I am fairly sure that it is to do with
incompatible versions
I am using
R 1.8.1
affy 1.3.26
affyPLM 1.0.0
AffyExtensions 0.6-2
which from the history line on Ben Bolstad's page
the regions of very low coverage. In some cases, the results that I obtained from CopywriteR shows a number -1073741823.5 (like below). I would like to confirm if this is in fact the result of very low read coverage of that region...it is a representation of -infinity as we're trying to calculate logarithm from around 0 or this number -1073741823.5 means something else.
chr6 28440001 28460…
updated 7.2 years ago • magdaaverte
file, DLLpath = DLLpath, ...) :
unable to load shared object
'/Library/Frameworks/R.framework/Versions/2.14/Resources/library/DNAco
py/lib
s/i386/DNAcopy.so':
dlopen(/Library/Frameworks/R.framework/Versions/2.14/Resources...library
/DNAco
py/libs/i386/DNAcopy.so, 6): Library not loaded:
/Library/Frameworks/R.framework/Versions/2.13/Resources/lib/libR.dylib
Referenced from:
/Library/Framework…
updated 14.5 years ago • Julie Zhu
div class="preformatted">Hi Gunter,
It appears that cn.mops has no mode for calling copy number segments
when just one sample is present.
Am I interpreting the documentation properly?
Thanks for the fine package
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updated 2.6 years ago • joseco8886
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pre>
> source("https://bioconductor.org/biocLite.R")
Bioconductor version 3.4 (BiocInstaller 1.24.0), ?biocLite for help
> biocLite("hta20sttranscriptcluster.db")
BioC_mirror: https://bioconductor.org...a/s/n]:
n
Warning message:
package ‘hta20sttranscriptcluster.db’ is not available (for R version 3.3.2) </pre>
Any ideas what the prob…
updated 8.9 years ago • ricardo.martinez-zamudio
424 641 478
Running DESeq2 using a simple additive design (~ age + qr) shows a large number of genes that are differentially expressed with age and a smaller number that are differentially expressed between...term: (~ age + gr + age:qr). We have strong *a priori* reason to think that there should be a large number of genes that respond differently to age in the treatment condition vs t…
updated 6.0 years ago • benjamin.aaron.taylor
Julie,
Julie Dickerson wrote:
> I am trying to figure out how to get the information about the
number of
> stat_pairs used in the MAS5 computations for each probe set. THis
> information does not appear to be in the exprsSet
updated 19.0 years ago • James W. MacDonald
To the developers,
I was able to load and install systempiper in R version 3.1.2 yesterday.
But today, since we transitioned to SLURM, we have R/3.2.5 and the newest versions. I was trying to install...thus we don't have the slurm.tmpl.
Is this because the systempiper needs to run on an older version of R?
Please advise.
Asher
updated 8.2 years ago • tarun2
78.65631 1.833459e-15 5.077535e-12
25.66512
any ideas?
thanks
paolo
[[alternative HTML version deleted]]
</na></na></div
div class="preformatted">Dear Simon,
Through biocLite, Bioconductor is installing version 1.4.1, which
doesn't
have function estimateDispersions. My R version is 2.13.0. I am trying
to
install version 1.5.17...office: 28253)
email:andreiaamaral@fm.ul.pt ; andreiaamaral@fc.ul.pt
[[alternative HTML version deleted]]
</div
updated 14.4 years ago • Andreia Fonseca
plotRanges didn't work In that version 4.0.0, and need the help for that, thank you alotv
updated 5.4 years ago • aissabenyoucef
> ''' BiocManager::install("clusterProfiler", INSTALL_opts = '--no-lock') '''
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.2 (2020-06-22)
Installing package(s) 'clusterProfiler'
trying URL 'https://bioconductor.org/packages/3.11/bioc/bin/windows/contrib/4.0/clusterProfiler_3.16.1.zip'
Content type 'application/zip' length 701307 bytes (684 KB)
downloaded 684 KB
packa…
updated 2.2 years ago • nilanjanamani88
Dear all,
I use the missMethyl package with the gometh and gsameth function to analyze whether significantly differentially methylated CpG sites are enriched in gene sets.
gometh can either analyze GO or KEGG genesets, whereas gsameth is a more generalized version where one can manually specify the genesets to be analyzed. In my analysis I used both gometh and gsameth w…
updated 9.7 years ago • philipp24
the it like this " iBBiG(mydata, nModules = 100, alpha = 0.3)"\] I always get a different number of significant clusters (something like 33±6). Is there any easy way to account for this variability? Should I try to integrate
updated 7.6 years ago • luca.zoccarato
preformatted">Hi everybody
I'm getting some discrepancies between results from affycomp package
(version 1.10.0, R version 2.4.1 Ubuntu box).
Briefly if I use the affycomp.R code within my machine, using the
installed package...AUC, med AUC and high
AUC (from
accessSpikeIn2), compared to the exact same data uploaded to the web
version of affycomp.
All the others results are the same.
Any su…
I cannot get bioimagetools package to install in R. I am using the latest version (3.5.1 as of this writing 2018SEP26). I updated from 3.5.0 because I thought that was the hangup. The hangup, however...I cannot get bioimagetools package to install in R. I am using the latest version (3.5.1 as of this writing 2018SEP26). I updated from 3.5.0 because I thought that was the hangup. The hangup, howev…
updated 7.2 years ago • jblument
terms for my data set. However, when I attempt to match my genes of interest with the GO terms, the number of genes associated with each GO terms does not perfectly match the "Count" number of genes determined by GoStats. I have...Searching within the org.Mm.egGO annotation
but none seem to perfectly match the expected count number. Has anyone else had a similar problem to this and have a soluti…
updated 9.2 years ago • adamgetzler
Hello
I have `RNAseq` of `miRNAs` so the number of tested miRNAs are `1640`
I have `2 healthy` samples versus `12 cancer` samples
Does it Statistically make sense to compare
div class="preformatted">What is the status/plans for software to compute copy number (NOT
genotype) from affy 500K chips in Bioconductor? I know about dChip
and CNAG but would like a non Windows solution
To The Developers,
I updated my R from version 3.3.2 to version 3.4.1 primarily so I can use the latest version of DESeq2 which is version 1.16.1
I'm using the tximport...nbsp;package to import transcript-level estimates. It was working before when I'm using R version 3.3.2 and version 3.3.2 but my DESeq2 version is still 1.14.1 so I decided to update my R version.
Upon running the tximport...…
updated 8.3 years ago • tarun2
Hello.
I'm trying to use copywriteR for calculating copy number across samples genome. My problem is that the program seem to be running for a short period of time until it
updated 9.5 years ago • thestaroceanster
Teen Patti Star customer care helpline number ✅ 7908285003
updated 2.6 years ago • Customer
Quick Money Loan Customer Care Number✍️ 8509079649 call
updated 2.6 years ago • Safe
Hello all,
Thanks to James W. MacDonald I was able to figure out how to convert NCBI forms to Enseml forms, however the database provided requires you to know the species before hand (library(org.Hs.eg.db), where Hs is Homo sapiens). I can't seem to find a database that compiles all species, nor can I find a tool that can take an accession number and translate it into its organism's name. I am us…
updated 2.1 years ago • j_denton
Problems installing S4Vectors using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1
Dear BioConductor team,
I am having problems installing the package "S4Vectors" using the latest versions of R and BioC (see below). Judging from the posts here, this seems to be a recurrent problem. Thanks for any help, Best,
Achim...nbsp;
> biocLite("S4Vectors")
BioC\_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.5), R version 3.2.1.
Insta…
updated 10.4 years ago • tresch
RUVr, my PCA plot shows a much better clustering based off of genotype and timepoint. However, the number of upregulated DEGs I get (padj<0.01 and LFC>0) almost doubles for each comparison I make. Is RUVr overcorrecting
Hi,
I'm using the incredible genvisR package to plot copy number data, using the cnSpec function.
In another script, I did a clustering analysis of this data.
I tried to change the order
updated 7.5 years ago • cedric.vmdl
<div class="preformatted">I randomly sucked in a bunch of old HumanMethylation27k files into the
shiny
new beadarray package (which is great, by the way) and saw:
> summary(nObservations(bsd)[,1] - nObservations(bsd)[,13])
Min. 1st Qu. Median Mean 3rd Qu. Max.
-6.000000 0.000000 0.000000 -0.004919 0.000000 8.000000
> colnames(nObservations(bsd))[c(1…
Has a final decision been made on the version of R to be used for the upcoming Bioconductor 3.1 release? It looks like it's on track to be R-3.2 but since that is...p/62531/#62532) says that Bioconductor 3.0 will be compatible with "any future version of R-3.1.x" which made me think that the choice for 3.1 would be R-3.2, but then I realized that's not exactly a statement
updated 10.8 years ago • David Eby
<div class="preformatted">Hi,
I am trying to install the the latest rtracklayer version from svn,
it's revision 50298.
But that doesn't install:
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared library '/Library/Frameworks/R.framework/Resou
rces/library/rtracklayer/libs/x86_64/rtracklayer.so':
dlopen(/Library/Framewo…
updated 15.1 years ago • Michael Dondrup
about a year ago, we installed R1.7.1 and bioconductor (updated at
that
time, not remember the exact version though) on one of our servers.
and now
i need to install R and bioC on a new server. I tried R1.9.0 and the
most
updated bioC...result in new format. So, could somebody
please provide some advice about how to install an older version of
bioc
packages ( in mycase, multtest) ?
many thanks!!…
div class="preformatted">Hi, there,
We are trying to identify genes conserved in 5 eukaryotic species but
not in
3 other eukaryotic species.
Is there a way to do it with some websites...Bioconductor
tailored
for this?
Your suggestions will be appreciated.
[[alternative HTML version deleted]]
</div
updated 15.8 years ago • Cheng-Yuan Kao
for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.17 (BiocManager 1.30.21), R 4.3.0 (2023-04-21 ucrt)
Installing package(s) 'org.Um.eg.db 'org.Um.eg.db'
Installation
updated 2.4 years ago • Cristina Lizbeth
supposed to be a Granges object of the ATAC peaks to search through or a list motif binding sites identified by matchPWM()? I’ve been using matchPWM to find instances of the motif across the genome and then intersecting this...these categories is calculated. In addition what is the range for binding? I'm assuming the higher number the but I don’t yet have a grasp on what constitutes “binding”.
…
updated 6.3 years ago • Nick Gomez
variable analysis.
I have a large RNAseq data set on a heterogenous population and I'd like to identify the major hidden sources of variation so that I can adjust for them when performing differential gene expression...pick the surrogate variables that explain most of the variation? And how do I determine what a good number of variables to pick is?
Thanks,
Doro
 
updated 9.2 years ago • nicklesd
<div class="preformatted">Hi all,
I have a list of mapped sequence reads to hg18 for that I have the
exact chromosomal location on NCBI build 36.
Cluster ID Strand Chromosome Cluster_Begin
Cluster_End
slc754_chr2 + chr2 74295624
74295644
slc4695_chr1 - chr1
203949843 203949866
slc2213_chr8 …
Hello everyone,
I would like to have some help to a retrieve a matrix or add additional features to the DiffBind heatmap.
So fare, I am using the DiffBind R package and I would like to show the correlation factors in the heatmap as numbers in the different tiles or as an alternative save the matrix, which is used to generate the heatmap to take the correlations factors from there.
I am using…
updated 4.1 years ago • Katrin
Treatment 1, Treatment 2, Treatment 3, Treatment 4, Treatment 5.
![Metadata][1]
The goal is to identify DEGs between each treatment and the control. I initially built the dds object with the raw counts from all groups...and then specified the pairwise comparisons of interest. However, I soon realized that the number of DEGs for each pairwise comparison is greatly influenced by whether I constru…
updated 2.5 years ago • sean.mccutcheon
Hello
I'm working with the ViSEAGO package and am using the function Custom2GO to make a database to use for Enrichment Analysis down stream. I have a column labled GOID that contains all of my go id numbers. My problem is that some of the numbers are able to map to GO.db and others are not yielding an error...
Is there a way for me to verify which of 360,000 GO ids are in the GO.db? right now…
updated 4.4 years ago • jabbar_campbell
preformatted">Hi all,
>From the output of a custom HMM routine,
I have data showing chromosome number and nucleotide position,
but no associated gene name or database identifier. e.g.
> logRiList[[1]][1:10,]
chromosome position...3
10 1 320085 320085 0.7877 3
How can I map this data to RefSeq Accession number or EntrezGene ID
etc. so
I can get the name of th…
2315.6
where according to the README:
SNP_NUMBER = Affymetrix internally assigned reference number
SNP_NAME = Affymertix SNP identifier
PMS = Perfect match (sense) intensity value
MMS = Mismatch (sense) intensity value...MMA = Mismatch (antisense) intensity value
Does anyone have any idea on how I can get the copy number from this
data?
Tried all the possible ratios but…
Hello,
I am very pleased that you provide docker images of bioconductor, I think this is a huge added value for your users.
I may have missed something, but it seems that they are some missing information in the docker tags.
From what I understood, there is no easy way to get a docker for one specific bioconductor release.
I mean, today, if I get bioconductor/release\_base it will be the 3.1 …
Hi,
Can anyone help me to solve my title question? I can not load DESeq2 in R version 3.3.3 in MacBook
Thnks
updated 8.1 years ago • daqu2010
Hello,
I have RNA-seq experimental data with the following variables (and the number of each in parentheses):
1. Treatment (3)
2. Distance from base (9 per repetition)
3. Repetition (4 per treatment)
To be clear, for...Hello,
I have RNA-seq experimental data with the following variables (and the number of each in parentheses):
1. Treatment (3)
2. Distance from base (9 per…
updated 4.5 years ago • erik.burchard
div class="preformatted">Hello Steffen and others,
Has the capability of searching older versions of Ensembl been added
to
the R version of biomaRt yet?
Thanks,
Lynn Amon
</div
I then put the read count values into a text file. The first column of the text file had the gene identifiers and each of the following columns contained the read count data for each of the 39 samples of the dataset.</span...t(x) %\*% (x)) : __
__ system is computationally singular: reciprocal condition number = 3.53861e-17__
Please advise on how I should fix this.
here i…
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