Bioconductor Forum

I apologize if this is a duplicate question,I read limmas paper (filtering section) it referred that after normalizing microarray data, for downstream analysis, it is usually worthwhile

DEG Limma Filtering

updated 9.7 years ago • Shamim Sarhadi

develop some tools in order to implement the ideas presented by P. Toronen in his BMC Bioinformatics paper: "Selection of informative clusters from hierarchical cluster tree with gene classes" 2004, 5:32 Before starting I would

updated 18.5 years ago • Ariel Chernomoretz

Hi, I have gone through your paper, Inferring Somatic Signatures from Single Nucleotide Variant Calls and I want to run somatic signature package on

somatic signature

updated 9.9 years ago • sj1

people's attention to the section entitled "Programmer's Reference". The intent is to provide papers and guidelines that provide useful tips to R programmers. Currently there are only a few documents in this section

PROcess PROcess

updated 22.1 years ago • Jeff Gentry

interested to annotate most significance exons, querying PFAM and SMART databases according with the paper "Detecting differential usage of exons from RNA-Seq data", supplementary figure S4. How did you compute them? Thanks in

annotate annotate

updated 12.7 years ago • Vincenzo Capece

rather I am interested in variability of gene expression within each condition. I have seen several papers addressing this, and even this recent package: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5737414/ . However, I would

deseq2 variation

updated 5.6 years ago • dannyc

contrast, the log2FoldChange and lfcSE are affected by shrinkage. As I understood from the DESeq2 paper (Love et al., 2014) to get the z-statistic, the LFC is divided by its standard error (the stat column in the obtained DataFrame

deseq2

updated 6.5 years ago • haasroni

be fully exploitable? 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

CRISPRseek

updated 4.1 years ago • nderian

filename = "GSE7535_family.soft.gz") geData <- Table(gds) 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 locale

GEOquery

updated 4.4 years ago • pedram_torabian

treat(fit,<strong>lfc=log2(1.1)</strong>,trend=TRUE) # a fold-change cutoff as proposed in the TREAT paper top <- topTreat(fit2, coef=2, adjust.method="fdr",p.value=0.05, confint=0.95, number=nrow(fit2))</code></pre> 1) I noticed, that when...differ), as also the __t statistic __( i did not mention the p-values, which are explained in the paper). Thus, this is a c…

limma treat topTreat microarray

updated 9.6 years ago • svlachavas

I was following the code from the paper "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and...I was following the code from the paper "Bioconductor workflow for single-cell RNA sequencing: Normalization, dimensionality reduction, clustering, and lineage inference". But I Encountered an error with the function assayData() during the pre-…

assayData() scRNA-seq single cell sequencing assayData Bioconductor

updated 5.5 years ago • Wagaa

Job reference: BMH-017047 Location: Oxford Road, Manchester, UK Closing date: 19/08/2021 Salary: £32,816 per annum Employment type: Fixed Term Faculty/Organisation: Biology, Medicine & Health School/ Directorate...Molecular & Cellular Function Hours per week: Full Time Contract Duration: 01 August 2021 until 31 July 2024 This is a Postdoctoral Research Associate oppor…

CancerData StructuralGenomics VirusStability pH-dependence

updated 4.3 years ago • jim.warwicker

these SNPs with my R session (sessionInfo() is the following): R Under development (unstable) (2021-02-23 r80032) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042) Matrix products: default...a` output is: Linux platonesrv1 5.4.0-66-generic #74-Ubuntu SMP Wed Jan 27 22:54:38 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux How could …

biomaRt

updated 4.7 years ago • Federica

Good evening to everyone! The limma package (and the related papers) defines the "random effect" in a mixed effect model as a "variable" (e.g. "patient_ID"). However, the lme4 package define the

limma lme4 mixed

updated 3.1 years ago • leandro

the best normalization procedures. RMA seems to be the standard in literature, however some papers have been opting away from global normalization procedures: - https://www.nature.com/articles/s41598-020-72664-6 - https

rma background microarray normalization

updated 4.1 years ago • Joshua

div class="preformatted">Dear List, Several papers on analysis of microarrays mention saturation as a problem in some microarrays. I was wondering what standard practice

probe probe

updated 20.5 years ago • McGee, Monnie

div class="preformatted">Hi all, I recently came across a paper (Maria Chahrour, et al. MeCP2, a Key Contributor to Neurological Disease, Activates and Represses TranscriptionScience

updated 17.5 years ago • affy snp

Bioconductors Friends, I have a question that I dont found answer for it. Please, if you have a paper/article that explain it, please, tell me. I normalize our data using normalize.quantile function. If I previous transform

limma limma

updated 20.7 years ago • Marcelo Luiz de Laia

I have these pathways in BioPAX format (downloaded from WikiPathways). I notice that the graphite paper talks about conversion BioPAX to SIF, but the package does not seem to provide a method to do the conversion, but rather

Pathways graphite Pathways graphite

updated 11.6 years ago • Ryan C. Thompson

works ok and I can obtain the Bs, Ns, Fs and the lambdas. I want to use equation 1 in the paper Li Zhang, Michael F. Miles and Kenneth D. Aldape - A model of molecular interactions on short oligonucleotide arrays, 2003

updated 22.2 years ago • Stephen Nyangoma

am using the enrichKEGG function. While I understand what the q value is (at least according to this paper:https://www.nature.com/articles/s41596-018-0103-9), what I don't understand is what the pvaluecutoff is. Is that the cutoff

KEGG RNAseq

updated 6.2 years ago • sportiellomike

wondering if anything can be done with control genes. Does anyone have any suggestions, pointers to papers, or a template script? The key feature is, of course, the complete confounding, so that it seems Combat or SVA are not applicable

sva sva

updated 13.3 years ago • Juliet Hannah

Hi, I have read this recent paper:  Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V, Wrobel N, Gharbi K, Simpson GG, Owen-Hughes T, Blaxter

deseq2 deseq

updated 9.7 years ago • ribioinfo

the classes). One thing I'm not sure is how to compare them because, as I read from the gcrma paper, the expression values after the gcrma() routine are log(intensity) after background adjustment. My question is: Do I have

gcrma convert gcrma convert

updated 14.5 years ago • yotsawat pomyen

<div class="preformatted">hi all, sometime ago someone asked about thoughts related to the use of mismatch probes (MMs) in affy arrays. The developmental package gcrma provides an implementation of a version of RMA that uses MMs. It also uses sequence information. the new method appears to improve the performance of RMA in terms of accuracy (estimated fold changes are bigger). the method i…

affy gcrma affy gcrma

updated 22.4 years ago • Rafael A. Irizarry

expression assume, correct me if I'm wrong, independence of the tests. Does anyone have at hand any papers on the performance -- in terms of type I error -- of methods such as limma / eBayes? I'm sure this issue has been investigated

limma limma

updated 13.4 years ago • January Weiner

I am confused about the log2FC when I use the limma to analyze the RNA-seq data. In the paper (Law et al. 2016; https://f1000research.com/articles/5-1408 ),  Log2FC of the gene (ENTREZID:12759) is -5.44 in&nbsp

limma

updated 7.2 years ago • zhouqz

dementia (FTD) and Alzheimer’s disease (AD). Our recent work ([Månberg et al. Nature Medicine 2021][1]) showed that vascular and glial cells contribute to the dynamics of neurodegeneration and this project will aim to

ATACSeq multiOmicsViz scRNAseq JobPosting

updated 3.4 years ago • Sebastian Lewandowski

with the 'pd.mirna.4.0' package. ``` R and Bioconductor environment: ```r R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE

affycoretools

updated 4.1 years ago • Gerhard Thallinger

stype), groupnames=levels(stype)) ``` R and Bioconductor environment: ```r R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 locale: [1] LC_COLLATE

affycoretools

updated 4.1 years ago • Gerhard Thallinger

dementia (FTD) and Alzheimer’s disease (AD). Our recent work ([Månberg et al. Nature Medicine 2021][1]) showed that vascular and glial cells contribute to the dynamics of neurodegeneration and this project will aim to

SpatialData scRNAseq SingleCell Omixer

updated 3.9 years ago • Sebastian Lewandowski

command failed with code 1 (use -v to see invocation) ``` ``` > sessionInfo() R version 4.1.1 (2021-08-10) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Big Sur 11.3.1 Matrix products: default BLAS: /Library

SC3

updated 4.2 years ago • krp

of items to replace is not a multiple of replacement length > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 21343) Matrix products: default locale

HTqPCR

updated 4.7 years ago • Nghia

in looking at the genes that are marked as dispersion outliers. I find in the Love et al., 2014 paper that a gene is considered as a dispersion outlier "if the residual from the trend fit is more than two standard deviations...seems a little less are marked as dispersion outliers. I understand from the description in the paper that this cutoff is made according to the standard deviation. I d…

Dispersion DESeq2

updated 2.6 years ago • raya.fai

and the European Commission through the e-Lico EU project. Participants are expected to prepare a paper, maximum 8 pages, describing their approach. We plan to have a number of selected papers considered for publication in

updated 15.2 years ago • Adam Woznica

time) and were in the form provided in the golubEsets package (and that was what they used in their paper). You could try writing to the authors of the paper to see if CEL files are available, they would be very old (6800s, and may

Cancer Cancer

updated 19.1 years ago • rgentleman

CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10) Old packages: 'boot', 'class', 'cluster', 'digest', 'foreign', 'ggpp', 'htmltools', 'jpeg', 'jsonlite', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet...CRAN: https://cran.rstudio.com/ Bioconductor version 3.14 (BiocManager 1.30.19), R 4.1.1 (2021-08-10) Old packages: 'boot', 'clas…

cdf

updated 3.0 years ago • Charmy

Hi everyone, I have read the paper of MAST and I also looked through the issues on github, but I still don't understand how MAST calculates log fold-change

MAST

updated 3.3 years ago • Chenghao

and didn't finish yet. Is it normal ? it consumes most of RAMs 8Gb and 31% cpu. However, I read in papers that clustal-omega can align >50000 seq in few hours. How can I apply this and what are the resources required to get

msa

updated 4.0 years ago • Radwa

All,  I am working on Micro-array data analysis  with this GEO acc no. GSE31747, In this paper PMID 22024983 (https://www.ncbi.nlm.nih.gov/pubmed/22028943) they have used ANOVA method to identify the significant

limma microarray

updated 9.0 years ago • mathavanbioinfo

based on comparison of variance and ICC among replicated arrays. However I can not find lots of papers which have applied these methods on Agilent data. I am looking forward to hearing from u. Regards, Samaneh Fazeli -- output

Normalization Normalization

updated 11.3 years ago • Guest User

to understand why the genes are filtered out on normalization step, it was hard to grab with the paper and vignettes. Could you explain to me a little bit easier way about this? Thanks in advance

deseq2 normalization

updated 6.6 years ago • yura.song

estimate. Default value being used.</span> I understand the default value is 0.5.  In the paper for metagenomeSeq, there's a citation that suggests using 0.75 for RNASeq data, but our data are shotgun metagenomic

metagenomeSeq microbiome

updated 10.9 years ago • noelle.noyes

normalized Affy expression data and keep the genes in the high 50% of variance, but saw the recent paper on an algorithm called FLUSH in NAR that filters on probe level data. What is the recommendation of the collective BioC

probe affy probe affy

updated 4.6 years ago • Dennis.Burian@faa.gov

trying to find out whether there are other methods or tools available. Any suggestions or relevant papers/pointer will be very helpful. Thank you for your time Diwan

transcription factor tf activation gene regulatory network gene expression

updated 9.0 years ago • Diwan

processed. Has anyone a hint? It is not just the difference of the mean like in limma. Even in the papers of breitling there is no good hint. best regards?, Georg Hildebrand -------------------------------- Contact/Kontakt: -------------------------------- Abteilung/Dept.:11100ho Web: http

limma limma

updated 15.8 years ago • Hildebrand, Georg

div class="preformatted"> The methodology paper on which the clippda package is based may be accessed from the following link: http://www.degruyter.com/view/j/sagmb.2012.11.issue

Genetics clippda Genetics clippda

updated 13.8 years ago • Stephen Nyangoma

conditions? (for example, under >10 different tissues or cell line experiments). I read all the papers/ documents I can find. But still not convinced we can use that assumption. Thanks Regards -h [[alternate HTML version deleted

Normalization Normalization

updated 22.7 years ago • Wang, Hui

affymetrix replicates each. (I will be using gcrma as preprocessing step) I seem to remember a paper that showed that T-tests did not predict known spiked-in changes better than simple fold change until one had 8 or more

Preprocessing gcrma Preprocessing gcrma

updated 21.6 years ago • Luckey, John

I have been following the paper ["Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"](https...I have been following the paper ["Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR"](https://f1000research.com/articles/6-2055) and I have some problems with the low count filtering process. #…

limma edgeR

updated 4.0 years ago • altintas.ali

have read them a bit too many times. My question is based on figure 5 from the spatial phenomena paper -- the workflow: http://www.biomedcentral.com/content/supplementary/1471- 2105-11-208-s5.pdf -- link to the paper = http://www.biomedcentral.com...requires care." -- how should one combine these tools with the material in the spatial phenomena paper? 3. Does one run generateNeighbours before r…

Cancer beadarray Cancer beadarray

updated 15.1 years ago • Anand Patel

been reading only SSPA allows for more than 2 groups. However, the example provided in the original paper only contemplates a microarray experiment with 3 conditions and is pilot-data based, data which I don't have. Has anyone

SSPA ssizeRNA RnaSeqSampleSize

updated 2.3 years ago • Megan

has 2 microarrays with dye swap, and we did the analysis using R limma package. When I submit the paper, the database asked for normalized data per each sample (biological replicate) for dye-swap experiment. But I only can

updated 16.8 years ago • fei tian

<div class="preformatted">Dear list, I'm using ALLMLL data set (from ALLMLL Bioconductor package). This package provides probe-level data for 20 HGU133A (MLL.A) and 20 HGU133B (MLL.B) arrays which are a subset of arrays from a large ALL study. I would like to know the phenotypic information about these data sets to run a differential expression analysis: I need the phenotypic info to group…

hgu133a hgu133a

updated 15.5 years ago • Javier Pérez Florido

gmail.com=""> wrote: > > Hi Michael, > > Do you happenly know there is any package or paper works for power calculation of factorial design of RNA-Seq project? Thanks. > > > Best, > > > Yanzhu </mlinyzh></div

updated 11.4 years ago • Michael Love

for any difficulties or wasted time this error may cause, and I'm very very sorry if you submitted a paper based on any erroneous data from my package. Sheepishly, -Ben</div

updated 20.8 years ago • Wittner, Ben

with shows where each of these genes are located. What is the best way to do this? Its for a paper so I need it to be of high quality. Thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis

Cancer Cancer

updated 16.1 years ago • Daniel Brewer

I am asking a question about scran, described in this paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0947-7 In the github code, low expression

filtering scran

updated 9.3 years ago • amckenz

clustering genes using RNA-seq data was not a well accepted practice. However, I have seen a paper using self-organizing map (SOM) algorithm to cluster genes from RNA-seq data. Any commentary or suggestion will be welcome

Network Clustering Network Clustering

updated 14.3 years ago • Biase, Fernando

div class="preformatted">In the paper and vignette describing the globaltest package, the authors mention the need for multiple testing when testing large

Pathways globaltest Pathways globaltest

updated 17.1 years ago • mpg33@drexel.edu