Bioconductor Forum

I am trying to create a working docker image (based on Shiny) which includes a BioConductor package. The packages are installed during the build phase, but they do not persist. I have tried installing it using 4 different methods ; none works. Dockerfile : ```r FROM rocker/shiny:4.0.5 RUN apt-get update && apt-get install -y \ libcurl4-gnutls-dev \ libssl-de…

docker

updated 3.3 years ago • Sam

CRAN: https://cloud.r-project.org Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22) **Installation paths not writeable, unable to update packages** path: /usr/lib/R/library packages: nlme, spatial, survival...c("rtracklayer", "IRanges", "GenomicRanges", type = "binary")) > sessionInfo( ) R version 4.2.0 (2022-04-22) Platform: x86_64-pc-linux-gnu (64-bit) Run…

rtracklayer GenomicRanges Installation

updated 3.5 years ago • Johanna

Hi, I am using apeglm to do Log fold change shrinkage to help during visualization of data, and after running `lfcShrink(dds, coef="condition_min_vs_control

apeglm

updated 2.4 years ago • Juan Pablo

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updated 13.8 years ago • Paul, Cristina

as a count matrix where row are regions and columns are sample IDs,I do not have access to bam files nor peak calls of these samples . Is it possible to use DiffBind to identify regions that are differentially accessible between

ChIPSeq ATACSeq differentially_occupied DiffBind

updated 4.5 years ago • pegah.taklifi

package example however I neither can find it anywhere in the bioc package or CRAN repositories nor does it seem to be part of the golubEsets package. Best regards, Benjamin Otto -- Benjamin Otto Universitaetsklinikum Eppendorf

updated 19.1 years ago • Benjamin Otto

Note that I cannot use any because I only have one matrix. I don't have any reference matrix nor do I have phynotype etc. Is there any package which allow me to define up or down regulated of my genes ?   Thanks &nbsp

microarray gene regulated differential gene expression

updated 10.9 years ago • Nemo

Submissions to present at Bioc2022 are now open. The deadline to submit is Tuesday March 29th, 2022. Please see https://bioc2022.bioconductor.org/submissions/ for more details. Cheers, posted on behalf of the Bioc2022

presentation Conference bioc2022

updated 3.8 years ago • shepherl

<div class="preformatted">And please, let's move these to bioconductor, they are of general interest rather than specific to the management of the project On Wed, Mar 27, 2002 at 12:22:39PM -0800, Anthony Rossini wrote: > Raf - it might be worth documenting your opinions on the matter, to start thinking of how the various approaches compare under different situations. Or is there a…

HIV HIV

updated 23.8 years ago • rgentleman

The Bioconductor Code of Conduct Committee updates, disseminates, upholds and enforces the [Code of Conduct][1] across all platforms of the Bioconductor project. Each year the Code of Conduct Committee invites applications to become a new member of the committee. If you are interested in becoming a member of the committee, please fill out the following short application. The applications are then…

conduct

updated 3.3 years ago • Laurent Gatto

LChadata <- read.flowSet(LChattodata) LChadata LChadatatrans <- transform("SSC-Log\_Height" = log10, "FSC-Log\_Height" = log10, "FL1-Log\_Height" = log10, "FL2-Log\_Height" = log10, "FL3-Log\_Height" = log10, "FL4-Log\_Height" = log10...FL5-Log\_Height" = log10, "FL6-Log\_Height" = log10, "FL7-Log\_Height" =log10, "FL8-Log\_Height" = log10, "FL9-Log\_Height" = log10, "FL10-Log…

gaussNorm issues null database

updated 9.6 years ago • Wilson Yeo

of my ChIP-chip analysis and tried to follow the tutorial (http://wiki.rglab.org/index.php? title=Public:RMAT). I have updated everything (R version 2.11.0 and rMAT version 2.4.0) and have downloaded the tutorial data file...Tapez 'contributors()' pour plus d'information et 'citation()' pour la fa?on de le citer dans les publications. Tapez 'demo()' pour des d?monstrations, 'help()' pour l'aide …

Preprocessing GUI rMAT Preprocessing GUI rMAT

updated 15.7 years ago • Patrick Schorderet

when I use the Bioconductor，i meeting some trouble. Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'FlowSOM' Package which is only available in source form, and may need compilation of C/C...Bioconductor，i meeting some trouble. Bioconductor version 3.15 (BiocManager 1.30.18), R 4.2.0 (2022-04-22 ucrt) Installing package(s) 'FlowSOM…

trouble

updated 3.4 years ago • 413014887

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Recognition Awards Bioc2022 Bioconductor

updated 3.7 years ago • shepherl

straightforward. All the contrasts you have proposed seem simple and sensible. There is no need nor possible advantage in subsetting the data. Best wishes Gordon PS. I haven't included you original post in my reply because

updated 11.5 years ago • Gordon Smyth

image for my purposes? Will I discover that VariantAnnotation is found in neither docker base nor docker core? But maybe somewhere else? Thank you

docker

updated 5.6 years ago • Paul Shannon

mi≡m), the sum $$Z = Y_1 + \cdots + Y_n \sim NB(nm\lambda, \phi n^{−1})$$ If we write out the log-likelihood, dropping terms that don't involve ϕ, we get: $$\sum\log \Gamma(y_i+\phi^{-1}) - n \log\Gamma(\phi^{-1}) + \sum y_i\log\left({\phi\mu \over 1...phi\mu}\right) + n\phi^{-1}\log\left({1 \over 1 + \phi\mu}\right)$$ Rewriting the log terms and rearranging gives us: $$ \sum\log \Gamma(y_i…

edgeR

updated 2.8 years ago • Dan

In addition, I'm afraid that overlapping regions (genes in common between pathways) would violate the assumption of independence in the multiple tests to correct for... Perhaps permutation of labels would be a better

deseq2 pathway analysis tximport

updated 7.8 years ago • Gon Nido

is strikingly different from the ChIP samples the underlying assumptions will probably be violated. So far I would normalize the data using the 10kb-bin strategy suggested in `csaw` to account for the compositional

csaw chip-seq

updated 6.1 years ago • ATpoint

to believe that this way of summarization would be wrong, but just wanted to confirm whether this violates any of the assumptions that DESEq2 makes? If this sound a valid approach, at what stage should this aggregation be

deseq2 tximport

updated 9.2 years ago • Chakravarthi Kanduri

be possible to somehow output between sample normalized TPM values for each gene or is this somehow violation a principle I am overlooking? Could I just divide the the TPMs from Salmon with the sizeFactors obtained from DESeq2

rnaseq deseq2 tximport salmon normalization

updated 8.6 years ago • kofoed

Hello everyone. I hate to ask questions about installing packages, but I really don't know what to do here. GO.db can't be installed on my device. Apparently R 4.2.2 is too new. ```r if (!require("BiocManager", quietly = TRUE)) + install.packages("BiocManager") Bioconductor version 3.16 (BiocManager 1.30.19), R 4.2.2 (2022-10-31) BiocManager::install("GO.db",dependencies=TRUE)…

GOexpress GO.db GOSemSim

updated 3.1 years ago • o.mattmann

CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Installing package(s) 'Herper' Warning message: In .inet_warning(msg) : package ‘Herper’ is not available for Bioconductor...doc/manuals/r-patched/R-admin.html#Installing-packages > sessionInfo() R version 4.1.3 (2022-03-10) Platform: x86_64-apple-darwin17.0 (64-bit) Running…

Herper

updated 3.8 years ago • e.everman

bioconductor.org/packages/release/bioc/html/oneSENSE.html) is still well maintained as of 14/6/2022? Or are there new updates on the package that I missed out on? Because right now the package doesn't seem to be functional

oneSENSE

updated 3.6 years ago • George

Hi everyone, I'm having trouble installing DEGreport due to a dependency: ``` > BiocManager::install("DEGreport") 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 (2022-06-23) Warning message: package(s) no…

DEGreport

updated 3.3 years ago • marinaw

Hi all, I encountered a strange problem running the "Analysis of public data using GEO" part of the code from the BeadArrayUseCases vignette: <pre> library(GEOquery) library(limma) library...Hi all, I encountered a strange problem running the "Analysis of public data using GEO" part of the code from the BeadArrayUseCases vignette: <pre> library(GEOquery) l…

BeadArrayUseCases

updated 9.8 years ago • smt8n

online to find examples, but none really talk about using the EXP files thare included in the zip. Nor are there good step by step examples

CEL RAW geoquery readaffy

updated 11.2 years ago • PyPer

any general AC trie implementations in another R package? My Google searching turned up nothing (nor for Commentz-Walters

Biostrings

updated 9.4 years ago • matt.chambers42

features (some pA sites nearby each other are clustered together) or with adjusted p-values or with log fold change values. Some specific sites also appear (to my eyes) to have very similar counts, but different dispersion estimates...estimateDispersions( dxd, formula = formulaFullModel) plotDispEsts( dxd ) R version 4.2.1 (2022-06-23) Platform: x86_64-pc-linux-gnu (64-bit) Running under:…

DESeq2 DEXSeq

updated 10 months ago • Elijah

It looks like tailgate was removed in 2022 on the RG lab GitHub page but is still listed in the package vignettes. Running gt_list_methods() shows cytokine gate...It looks like tailgate was removed in 2022 on the RG lab GitHub page but is still listed in the package vignettes. Running gt_list_methods() shows cytokine gate as

openCyto

updated 15 months ago • ztflaten

is that some years ago the devs set`` bFullLibrarySize=TRUE ``as default to guard against violation of the assumption that the majority of enrichment regions were similar between groups. This has not been updated

diffbind chip-seq normalization deseq2 tmm

updated 9.0 years ago • siklenkak

R. I have found *some* sites that suggest it should be possible, but neither Limma (read.maimages) nor marray seems to recognize this fileformat (I've consulted the help files, naturally). As far as I know I am working with the

limma limma

updated 22.2 years ago • Edo Plantinga

By looking through the perl scripts I realized that I should not have quotes around my probe ids nor my accession numbers. I edited my file in openOffice's calc which automatically adds those pesky quotation marks. Since

probe probe

updated 19.5 years ago • Craddock, Richard C. CDC/NCID/VR CTR

substitution matrix using Gonnet Warning in f(x) : NAs introduced by coercion 7 %Warning in log(a) : NaNs produced 9 %Warning in log(a) : NaNs produced 11 %Warning in log(a) : NaNs produced 13 %Warning in log(a) : NaNs produced 15 %Warning...in log(a) : NaNs produced 16 %Warning in log(a) : NaNs produced 18 %Warning in log(a) : NaNs produced 25 %Warning in log(a) : NaNs produced…

dnds R msa

updated 3.1 years ago • 969183828

contrast = c(1,-1,-1,1))``` I was wondering how to interpret the output. In particular, does the log fold value give me log(A)-log(B)-log(C)+log(D) = log((A/B)*(D/C))? Setting lfcThreshold then gives a threshold on the above value? Thank you

DESeq2

updated 24 months ago • pl23

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updated 3.7 years ago • shepherl

workflow into a Bioconductor package. I'd like to release with the next release cycle (October 2022). When should I submit my package to do this? Is there a submission deadline for the October release? Finally, how long does

Devel

updated 3.6 years ago • Jonathan

datasets and would like to compare their raw read counts. Their correlation: cor(log(data$set1), log(data$set2)) 0.8734045 cor(data$set1, data$set2) 0.2376726 I have tried to plot them (raw read count and log transformed...I have attached pictures.![log correlation plot][1] ![raw counts][2]![enter image description here][3] The log transformed plot look weird. Did I …

plot correlation

updated 6.2 years ago • annkolman78

50) When I checked the warnings it showed > warnings() Warning messages: 1: NaNs produced in: log(x, base) 2: NaNs produced in: log(x, base) 3: NaNs produced in: log(x, base) 4: NaNs produced in: log(x, base) 5: NaNs produced in: log(x, base) 6...NaNs produced in: log(x, base) 7: NaNs produced in: log(x, base) 8: NaNs produced in: log(x, base) 9: NaNs produced in: log(x, base) 10: NaNs pr…

probe probe

updated 21.2 years ago • Lizhe Xu

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 using R. Thank you for any

AccNo OrgDb convert Organismname RStudio

updated 2.2 years ago • j_denton

is build from a very diverse set of sources and a significant number of entries has neither GenBank nor RefSeq IDs. The question to more advanced users is now: how would you proceed in this case? Is there a way to pull in Info using

Annotation GO AnnBuilder Annotation GO AnnBuilder

updated 18.9 years ago • Johannes Graumann

<div class="preformatted">Hello list members package biomaRt requires RCurl package, but I didn't manage to find it anywhere... It is not existing in package listing neither on the cran.r-project.org nor on bioconducor, Does anybody have a clue? Regards Vladimir -- Krasikov Vladimir Universiteit van Amsterdam Faculty of Science...to find it anywhere... It is not existing in package list…

biomaRt biomaRt

updated 19.7 years ago • krasikov@science.uva.nl

as a whole). Do you have any thoughts on this or are there required assumptions I'd be blatantly violating that makes this seem like a poor idea? happy sunday, Mike

deseq2

updated 9.0 years ago • AstrobioMike

values. ***First, is this a an appropriate task for differential expression analysis, or does it violate any rules within DEG analysis?******* My data has two treatment groups, each with 7-12 subjects. If I remove the outliers ( | NormalizedCounts

deseq2 outlier normalization removal

updated 5.8 years ago • knholm

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probe probe

updated 13.7 years ago • Paul, Cristina

CRAN: https://rweb.crmda.ku.edu/cran Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.3 (2022-03-10) Did it even install? If it didnt install how do I fix this

BiocManager

updated 3.8 years ago • Kelly

the data. Error in getControlData(controlData, type = "data.frame") : Can't find controlData slot, nor do the TargetID looks like control probes > Thanks & Regards KUNAL GAURABH JHA JAIVIK DATA CONSULTENCY [[alternative

GO probe GO probe

updated 12.4 years ago • kunal jha

0.000000 1023 $P2 SS INT LIN SS 1024 0.000000 1023 $P3 FL1 INT LOG CD103 FITC 1024 1.000922 10000 $P4 FL2 INT LOG CD10 PE 1024 1.000922 10000 $P5 FL3 INT LOG CD13 PE-CF594 1024 1.000922 10000...P6 FL4 INT LOG CD5 PC5.5 1024 1.000922 10000 $P7 FL5 INT LOG CD11c PC7 1024 1.000922 10000 $P8 FL6 INT …

flowcore

updated 10.2 years ago • Thomas67

Hi, I am learning the DESeq2 package. I have derived the log likelihood function in the negative binomial distribution, that is,  ![](http://latex2png.com/output//latex_8dc9ae8d557f57666b91ea4917e5e664.png...In the log\_posterior function, the log likelihood part is <pre> ll_part = sum(lgamma(y + alpha_neg1) - Rf_lgammafn(alpha_neg1) - y * log(mu + alpha_neg1...alpha_…

deseq2

updated 8.6 years ago • vtshen

Dear Bioconductor Community, i would like to ask for a specific question(maybe a bit) naive regarding the interprentation of log-fc values of specific contrasts from my object created after the eBayes function. In detail, i have performed a paired analysis in limma regarding cancer vs adjucent control samples-60 samples and in total 30 patients __condition <- factor(eset.2$Disease, leve…

limma logfoldchange limma design matrix paired samples affymetrix microarrays

updated 10.3 years ago • svlachavas

selecting in-person attendance from the pool of applicants. The lottery begins this Sunday May 15, 2022. Please [register for the lottery](https://bit.ly/Bioc22Tickets) as soon as possible. More registration details can be found

Registration Bioc2022 Conference

updated 3.7 years ago • shepherl

https://forms.gle/u7iWAiRUYaB8pR4H8) to nominate someone. The deadline for nominations is May 20, 2022

Bioc2022 Awards Bioconductor Recognition

updated 3.8 years ago • shepherl

Is there a way in limma of obtaining the least variable genes per technical rep set (which I guess violates independence somewhat as the 4-6 replicates are done on the same individual), and then comparing these results to

limma limma

updated 22.1 years ago • Simon Melov

have more influence. To check this, look for abnormalities in the heatmap and also look for gross violations from normality in the prior plots generated by ComBat. Thanks! Evan On May 22, 2014, at 4:33 AM, Giuliano Stirparo <giulianostirparo

Microarray Microarray

updated 11.6 years ago • W. Evan Johnson

predictable genes and gene families were turned on or off), but it definitely seems like it could violate some underlying statistical assumption of RNA-seq. Is there anything to consider when trying to analyse data such

rnaseq deseq2

updated 7.4 years ago • Poikilo

Thanks > library(biomaRt) > listMarts(host="www.ensembl.org") Space required after the Public Identifier SystemLiteral " or ' expected SYSTEM or PUBLIC, the URI is missing Entity 'nbsp' not defined Error: 1: Space required...after the Public Identifier 2: SystemLiteral " or ' expected 3: SYSTEM or PUBLIC, the URI is missing 4: Entity 'nbsp' not defined &…

biomart

updated 9.6 years ago • s.corley

in the same cluster, how could we explain about them? Some of them are neither marker genes nor differentially expressed genes of that cluster, why are they assigned to that specific cluster??? Thank you very much and

SC3

updated 8.0 years ago • angela.ubn

<div class="preformatted">Dear List, I have microrarray data where condition is completely confounded with a time batch effect. When doing a PCA on the RMA normalized data, the first principal component separates clearly the two batches. What option do I have when I still want to compare different conditions across batches? As far as I understood I can't dissolve this batch effect neither…

GO limma GO limma

updated 13.8 years ago • Tefina Paloma

This should generate significant synergies, which increases the chance of innovative research and publications (see below). In particular, the bioinformatics postdoctoral fellow will be involved in novel studies from the...unibas.ch). Applicants must upload a motivation letter and research interests, CV with complete publication list, grades of master and PhD and the names and addresses of three …

PostDoc JobPosting Basel Switzerland

updated 4.1 years ago • Robert Ivanek

CA,"ape::DNAbin") class(CA) <- "matrix" CA <- as.DNAbin(CA) a <- dnds(CA) Warning in log(a) : NaNs produced Warning in log(a) : NaNs produced Warning in log(a) : NaNs produced Warning in log(a) : NaNs produced Warning in log

R ape dnds nan nanotubes

updated 3.1 years ago • Working