Bioconductor Forum

lowess, quantreg, waveslim (or other packages) to analyze CGH or DNA copy number data? A recent paper in the journal Bioinformatics mentions these packages but not how they were used. Thanks ****************** soranim at pharmacy.ucsf.edu

CGH CGH

updated 20.3 years ago • Sorani, Marco

I'm using BSprepare function in R package MethylPipe to perform binomial test. The paper says "The resulting multiple-testing corrected p-values are stored on the disk in the Tabix compressed and indexed...I'm using BSprepare function in R package MethylPipe to perform binomial test. The paper says "The resulting multiple-testing corrected p-values are stored on the disk in the …

MethylPipe

updated 9.6 years ago • 746458071

<div class="preformatted">Hi, all I am a newbie to EdgeR. Now, I am following the introduction to EdgeR, and I need the training data set of Zhang, W et al. 1997. The link in the original paper doesn't work any more. was anyone able to locate this data before? If so, could you please Email to me? Thanks, Shaohua Fan </div...to EdgeR, and I need the training data set of Zhang, W et al. …

edgeR edgeR

updated 14.8 years ago • shaohua.fan

I tried to push changes from local master to upstream (bioconductor) for package RiboDiPA. However I received the following errors which I don't know how to correct. Anyone could give some hints? Thanks. ``` (base) jon@Jipings-2021-macbook-pro RiboDiPA % git push Enumerating objects: 17, done. Counting objects: 100% (17/17), done. Delta compression using up...which I don't know how to correct. A…

RiboDiPA

updated 12 months ago • Jiping Wang

C:/Sequence/SeqData/bam/A1.bam") Session Info as follows sessionInfo( ) R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041) Matrix products: default locale

Rsamtool Rsamtools

updated 4.6 years ago • jbzhang2012

any sort of a refund. When I asked to get a complete revision, he requested that I purchase another paper using the very same directions. The beginning of my critique at [superbpaper reviews][1], but what went downhill because...I purchased a newspaper . Super b Paper has excellent prices and a good service listing, however their grade and their service are horribly low. Provided that

gramm4R

updated 4.3 years ago • Steve

to identify any novel transcript isoforms as compared with Table 3 from data analyzed in the linked paper. The first thing I tried was to use no filter, but that did not work. I am wondering if there was an issue in how I fed the data...me from getting novel transcript isoforms as found in [Table 3][2] of the linked Nature protocol paper. Thank you so much. [1]: https://www.nature.com/arti…

isoform RNA-seq hisat2 stringtie ballgown

updated 5.2 years ago • ra711

div class="preformatted">Hello ... I downloaded the data for the Luo 2002 paper (GEDP accession 230) w/ the intent of building an exprSet out of the data. What they provide appears to be the .txt files output

updated 19.9 years ago • Jeff Gentry

way, please elaborate your answer because I am new in this field. or suggest some good papers on that. &nbsp

drug development pathways bioinformatics

updated 7.0 years ago • wajeehaejaz17

man page defines it as "\[...\]p-values for the alternative hypotheses mixed\[...\]", but neither paper cited mention what that alternate hypothesis actually means. Can anyone enlighten me as to what that p-value actually

limma romer

updated 7.8 years ago • johnmcma

reports. I am new to bioconductor, so any pointers towards libraries, functions, algorithms, or papers I could use would be much appreciated

fasta multi-species

updated 5.2 years ago • drew.neely

Hello, I'm currently working with package polyester, and I'm trying to modify the way that the number of reads per transcript is generated (readmat). I actually wanted to use a method inspired on DESeq2 (Materials and methods of the 2014 paper) using the distribution parameters a1, alpha0 and sigmad. It is why I wanted to know if you have a range of values (or the order...readmat). I actually wan…

polyester dispersion

updated 4.7 years ago • catalina.gonzalez-gomez

In DESeq2 paper: _edgeR \[2,3\] moderates the dispersion estimate for each gene toward a common estimate across all genes, or toward a local

deseq2 edger

updated 9.9 years ago • tonja.r

take a 5% cutoff on the adjusted p-values? (in fact, which one did you choose on your bayeseq paper for the real data analysis?) Thank you. Kind Regards Tina</div

Bayesian edgeR Bayesian edgeR

updated 13.8 years ago • Tina Asante Boahene

div class="preformatted">Hi, Today I read a paper in Plant Cell, and the researcheres used GeneSpring 4.2 software (Silicon Genetics, Redwood, CA) to nomalize their data

Genetics limma Genetics limma

updated 21.0 years ago • xpzhang

to set the y and x limits for Enhanced Volcano are no longer working. The vignette was updated 8/19/2021, but it looks like the syntax for adjusting the y and x limits was not changed. Can someone please help me figure out what...1) Warning message: Ignoring unknown parameters: xlim, ylim > sessionInfo() R version 4.1.0 (2021-05-18) Platform: i386-w64-mingw32/i386 (32-bit) Running …

DESeq2 EnhancedVolcano Bioconductor

updated 4.3 years ago • Rachel

for help > BiocManager::install() Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Old packages: 'pcaPP' Update all/some/none? [a/s/n]: a There is a binary version available but the source version is later...gt; BiocManager::install("flowAI") Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Installing package(s) 'flowAI' trying URL 'htt…

flowAI

updated 4.6 years ago • msoares

data. I think that DEXSeq could also be used to identify tissue-specific exons and in the following paper they do something similar: [paper][1] As a first step I try do identify differentially used exons in the retina by choosing

#Retina #RNA-Seq #DEXSeq

updated 3.2 years ago • osieman52

Enter the body of text here I am new to R (R version 4.3.0) and RNAseq. As tutorial, I am using the paper 'RNA-Seq workflow: gene-level exploratory analysis and differential expression [version 2; peer review: 2 approved]" by...everything seems to well until now, I have an error message stated below which worked well in the paper: ``` #Error in makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs…

rnaseqGene

updated 2.4 years ago • ikpa_p123

test), I got 5 significant pathways, with the top q-value of the order 10^-3. Although the original paper (Luo et al, 2009) claims, refering to Kim/Volsky 2005 paper, that for gene sets of 10 genes and more the assumption of normality

t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment

updated 9.4 years ago • smt8n

repetition). I wondered if there was a favoured way to normalise this data. The most cited paper I have found is the Vandesompele 2002 paper using the geometric mean of a number of control genes, implemented in R in

updated 17.3 years ago • james perkins

moderated median-t" (PLW) a try because the ROC curves on the spike-ins looked promising on the paper introducing it (http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2358895). First, I think that the function...about PLW (I'm not a seasoned statistician, so I probably missed some things when reading the PLW paper)? Thank you very much in advance for any help given. I really appreciate…

affy plw affy plw

updated 16.7 years ago • davidl@unr.nevada.edu

Hello! How did this paper (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6372280/pdf/elife-41930.pdf) categorize the pathways in figure 2D (see

gage RNASeq gageData Pathways

updated 3.7 years ago • OST

Hello, Greetings! I am new to RNAseq analysis and currently learning how to utilize R to determine the numbers of differentially expressed genes (DEGs) that are upregulated and downregulated. I have obtained some data from public papers, but I am uncertain about which R package to use with this normalized data. (I have attached the file.) Could you kindly assist...expressed genes (DEGs) …

rnaseqDTU RNAseq

updated 2.4 years ago • Nguyen

Hi Can anybody point out to a tutorial/paper which explains the normalization method used by edgeR? <span style="line-height:1.6">Another thing, though, TMM is the default

edger

updated 10.3 years ago • p_das

<div class="preformatted">Hi, I'm looking to perform a classification analysis on an imbalanced data set using random Forest and I'd like to reproduce the weighted random forest analysis proposed in the Chen, Liaw & Breiman paper "Using Random Forest to Learn Imbalanced Data"; can I use the R package randomForest to perform such analysis? What is the...I'd like to reproduce the we…

Classification Classification

updated 19.8 years ago • portnoy@supereva.it

on the basis of the noise sampling method designed by Sorin Draghici? This is with reference to the paper titled "Noise sampling method: an ANOVA approach allowing robust election of differentially regulated genes measured

updated 20.5 years ago • Ankit Pal

div class="preformatted">Hi all, I've just read the paper describing the GraphAT package, installed and loaded the package (1.12.0). I am now eager to apply it to my data, some predictions

Yeast GraphAT Yeast GraphAT

updated 17.6 years ago • Paul Shannon

I'm using Gviz to make read-coverage and Sashimi plots for a paper, and I'd like to extract information about how many reads contribute to each splice junction in the Sashimi plot. These

gviz sashimi

updated 6.2 years ago • willbradshaw

Hi there, i am stuck here in the analysis of mirna-mrna interactions because i migrate from deseq2 to mircomb and according to the paper of package you can add any format, but you need to have the specific columns if you want to do from DEGs/DEMs lists. They are...analysis of mirna-mrna interactions because i migrate from deseq2 to mircomb and according to the paper of package you can add any …

deseq2 mircomb degs dems

updated 5.4 years ago • andreia

There seems to be some problem with OSAT that doesn't return the same size of data that was used for input: ``` r library("OSAT") data(survey, package = "MASS") VoI <- c("Sex", "Smoke", "Age") n_batch <- 3 iterations <- 10 gs <- setup.sample(survey, optimal = VoI) gc <- setup.container(IlluminaBeadChip96Plate, n = n_batch, batch = 'plates') gSetup &am…

OSAT

updated 4.7 years ago • Lluís Revilla Sancho

div class="preformatted">Hi all, I am reading through a paper by Shadt, Li, Su & Wong: Analyzing High- Density Oligonucleotide Gene Expression Array Data. Journal of Cellular Biochemistry

updated 22.2 years ago • Stephen Nyangoma

apply your method `generateNull` from your package `singscore` and your NK cell signature from your paper "A gene signature predicting natural killer cell infiltration and improved survival in melanoma patients" (Cursons

singscore generateNull

updated 4.9 years ago • tiphaine.martin

approach that we could use to normalize our data based on the spike- ins? Can anyone recommend any paper covering that topic? Thank you for your help, Agnes </div

Normalization Normalization

updated 11.8 years ago • Agnes Paquet

I was wondering what the annotated/significant/expected columns are referring to? Is there a paper on this that would help me interpret results?  Thank you!&nbsp

topGO reults

updated 10.5 years ago • megerdes

I have a couple of questions about estimation of dispersion in DeSeq2 vs. DeSeq. The paper and manual on DeSeq and DeSeq2 are very clear but I have a hard time understanding what is the ‘correct’ or ‘recommended

deseq deseq2 rnaseq

updated 11.0 years ago • JK

set , and i normalized and read it using the code bellow , but my result is different from what the paper claim. library("limma", lib.loc="~/R/win-library/3.1") targets<-readTargets("target2.txt",row.names=1,sep="") targets$Filenames

limma agilent

updated 10.1 years ago • nvayin

methylation levels for my MBD-seq data. However, I do not have a matched ssl control. I saw the paper mention analysis without including the ssl control. However, I wasn't able to figure out how to do this. I can only do CpG

Baymeth methylation MBD-seq Repitools

updated 9.5 years ago • pm2015

It worth to notice that I don't find any relation between this gene and my hypothesis in texts and papers. I apologize for my minor question&nbsp

limma microarray DEG

updated 9.0 years ago • Shamim Sarhadi

Hi, a reviewer has asked us to compare some RNA dynamics between samples collected at steady-state. I have previously used INSPEcT+ with matched 4sU samples and now I want to try using INSPEcT- for some samples without matched 4sU samples. I took a look at the paper Furlan et al., 2020 Genome Res, which states that INSPEcT "can now unveil RNA dynamics from steady-state or time course data, wit…

INSPEcT

updated 2.9 years ago • MK

nar/article/40/10/4288/2411520/Differential-expression-analysis-of-multifactor> In Figure 2 of this paper, the authors show that estimating dispersion on a per-gene basis is more compatible with their data: ![Figure 2 of edgeR...paper](https://s3.postimg.org/rgqn5tew3/edge_R_figure2.png) (I realise I'm probably not supposed to copy the figure here, but

edger differential gene expression rnaseq

updated 8.7 years ago • gabriel.rosser

read the xz-compressed GFF file as a `data.frame` with `read.delim` ```r R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is...ID.gene00001.Name.EDEN <0 rows> (or 0-length row.names) > sessionInfo() R version 4.1.1 (2021-08-10) Platform: x86_64-pc-linux-gnu (64-bit…

rtracklayer

updated 4.3 years ago • Charles

it can be? Thank you in advance for your feedback. ```r > sessionInfo( ) R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19043) Matrix products: default

CRISPRseek

updated 4.0 years ago • nderian

ENTREZID") # heatmap: heatplot(edox, showCategory = 3) sessionInfo( ) ## R version 4.1.1 (2021-08-10) ## Platform: x86_64-apple-darwin17.0 (64-bit) ## Running under: macOS Big Sur 11.6 ``` ![enter image description here][1] Thanks

clusterProfiler enrichplot heatplot

updated 4.0 years ago • fatimaruizdelabastida

r > BiocManager::install("DESeq2") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4 (2021-02-15) Installing package(s) 'DESeq2' trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/DESeq2_1.30.1.zip

DESeq2

updated 4.7 years ago • reneclassens92

Dear developers of branchpointer, following the recommendations of a recent review paper on branchpoint prediction tools, we are using branchpointer in the context of alternative splicing. Generally, this

branchpointer

updated 3.8 years ago • Matthias Lienhard

logical? And if it is can you recommend me a method to calculate this. And also let me know about a paper for reference. Thanks

Rnaseq

updated 2.6 years ago • zaid ur

thesis I need to compare different normalization methods for flow Cytometry data. In an older paper 'Per-Channel Basis Normalization Methods for Flow Cytometry Data' Hahne and co. describe an algorithm called 'fdaNorm

flowStats

updated 4.3 years ago • Max

which can calculate "distance" or "similarity" between two gene lists with different lengths. Any paper, any implementation in R and any suggestion is welcome! Thanks, -- Weiwei Shi, Ph.D Research Scientist GeneGO, Inc. "Did you

updated 17.3 years ago • Weiwei Shi

In limma paper in 2015 (https://academic.oup.com/nar/article/43/7/e47/2414268), it stated that it accommodates unequal variances of different

limma treatment variance

updated 5.9 years ago • ML18

Hi! I am trying to run DMRcate with a dataset downloaded from a paper. This dataset consist, instead of a set of probe names and their corresponding beta values, of a set of genomic positions

DMRcate

updated 5.2 years ago • Jeni

of an RNAseq experiment. Therefore I requested the raw read counts instead from the author of a paper in order to analyse the conditions myself. However the author has only provided me with the Deseq2 normalised counts

deseq2 rnaseq

updated 5.7 years ago • n.anuragsharma

We would like to map data from a 2009 paper that has been deposited in the GEO database from a large "ChIP-chip" experiment looking at histone modification markers

bioconductor affy tilingarray

updated 9.0 years ago • jmtepp

PLIER package) are for background correction, normalization and summarization. I've read techical paper about justPlier and for background correction PM-MM and PMonly options are, for normalization "quantile" and don't know

Normalization Normalization

updated 15.5 years ago • Javier Pérez Florido

div class="preformatted">Hi Pelizzola, You have mentioned in your paper (Pelizzola et al, Genome.Res 2008) that DNA methylation data is not linear and you have used limma in your data analysis

MEDME MEDME

updated 16.6 years ago • Ashwin Kumar

gt; with an FDR objective. Not bogus. Just less important than some other considerations. > The paper by Bourgon et al. motivates filtering differently, namely by > using a filter criterion that is independent of the...under > the null (thus does not affect type-I error; some subtlety is discussed > in that paper) but dependent under the alternative (thus improves &a…

Microarray Preprocessing limma Microarray Preprocessing limma

updated 12.5 years ago • Gordon Smyth

sample can be considered as an outlier (instead of just by visual inspection of PCA, like most papers do). In a recent paper of Conesa et al  2016 ([https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016

deseq2 rnaseq PCA hierarchical clustering outlier

updated 9.0 years ago • wd

div class="preformatted">Dear list, I fellow a paper to annotate a snp in which part of a gene. I firstly think that GenomicFeatures transcriptsBy method. But it seems transcriptsBy...detail check. Does anyone have some suggestion? Thanks. The define of annotaion is fellow in the paper. 1, First (non-coding) exon. If the gene has at least 2 exons, this is the part of the first exon that is n…

SNP annotate GenomicFeatures SNP annotate GenomicFeatures

updated 14.5 years ago • Fabrice Tourre

assembly: https://bioconductor.org/packages/BSgenome.Hsapiens.NCBI.T2T.CHM13v2.0 Companion paper: "The complete sequence of a human genome" by Nurk S, Koren S, Rhie A, Rautiainen M, et al. Science, 2022. A SNPlocs data package

BSgenome dbSNP T2T-CHM13v2.0 SNPlocs

updated 3.6 years ago • Hervé Pagès

you faced with these kind of arrays? There is any specific statistical package? Or at least some papers to look up about the experimetal design ,strategy of Analysis and so on! Thanks for any help Daniela Marconi PhD student

updated 17.8 years ago • Daniela Marconi