Bioconductor Forum

Hi everyone I will be given certain illumina micro array gene expression data in couple of weeks. I am new to illumna microarray gene expression analysis. So I need to clear certain basics. I read certain research paper where they mentioned for analysis purpose lumi and beadarray from bioconductor is mostly used. My question is for raw...microarray gene expression analysis. So I need to clear cer…

microarray lumi

updated 9.8 years ago • kritikamish99

I am trying to find perturbed pathway from expression date using a kegg gene set. In the GAGE paper (Luo et al., 2009), iit is recommanded to use the option same.dir=F on KEGG pathwayt is worthy to run gage with  to capture

gage gene set testing

updated 7.5 years ago • Aurora

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 • Michael Gormley

the package inSilicoMerging, particularly to perform the COMBAT batch effect removal. The original paper http://www.biomedcentral.com/1471-2105/13/335 sort of advertises the package handles covariates. However there seems

inSilicoMerging inSilicoMerging

updated 11.6 years ago • François Lefebvre

416, 2016) about Quasi-likelihood methods in edgeR, but there was no mention paired designs in the paper. Is glmFit/glmLRT still preferred for paired designs? &nbsp

edger paired samples glm QL F-test LR-test

updated 9.3 years ago • Akira Imamoto

div class="preformatted"> Dear all, Recently I'm reading the paper "Moderated statistical tests for assessing differences in tag abundance"(http://bioinformatics.oxfordjo urnals.org

updated 12.1 years ago • Guest User

obtained from Agilent 8x60k chip for the analysis of mRNA expression. I have gone through lots of papers that describes only about Agi 4x44 chips. Here am facing a trouble of filtering the genes using the LIMMA package in

Normalization limma Normalization limma

updated 13.6 years ago • Muralidharan V

genome (already in a matrix) for differentially expressed genes between different samples. I found a paper listing the most recent bioconductor packages for this kind of analysis: <https://bmcbioinformatics.biomedcentral.com

rna-seq packages

updated 8.8 years ago • Maximilian

<div class="preformatted">Dear all, I have time course data (processed and have expression values as log2 fold changes) with and without drug at various time points. I want to do a clustering experiment with data. I read from various papers that before doing clustering, the data is normalized using mean, median or centroid mean. I have 2 questions: 1. Why do I...drug at various time poi…

Normalization Clustering Normalization Clustering

updated 17.8 years ago • kumar s

replicates without any additional variable of biological individual factor as like GLM. In the paper, one of published data sets for such kind of type data which has both tech and bio replicates was also analyzed: RNA-Seq...Sj, it is using geometric mean pseudo-reference as like quantile adjusted way in 2008 Robinson paper. so. here i was wondering why it is taken by especially geometric mean rat…

DESeq DESeq

updated 15.1 years ago • sunghee OH

div class="preformatted">Hi, I've been reading a few papers and I'm looking for some other opinions on a couple of questions/ideas I have. Basically this is directed towards a discussion...s. Naef & Magnasco. 2003. Phys Rev E 68, 011906. My understanding is that- The first of these papers shows that MM intensity is related to GC content, and weights MM values towards the average dist…

gcrma oligo gcrma oligo

updated 21.9 years ago • Matthew Hannah

of running the following in an R session sessionInfo( ) ```R version 4.1.0 (2021-05-18) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Matrix products: default BLAS: /usr/lib/libblas

EnhancedVolcano

updated 4.2 years ago • Raj

<div class="preformatted">Hi Anand, Many thanks for your interest in our work on spatial artefacts. Our current belief is to do things in the following order 1) Detect the phenomena described in the Smith et al (2010) paper. You do need to run generateNeighbours before many of these functions. The number of beads detected at this stage should be relatively small, and would probably be rem…

Cancer beadarray EBImage Cancer beadarray EBImage

updated 15.1 years ago • Mark Dunning

of transcripts: 33036 # Db created by: GenomicFeatures package from Bioconductor # Creation time: 2021-04-12 15:14:08 +0200 (Mon, 12 Apr 2021) # GenomicFeatures version at creation time: 1.42.3 # RSQLite version at creation time: 2.2.6...last_modified_t… etag <chr> <chr> <chr> <chr> <chr> <chr> <chr> <dbl> <chr> 1 BFC1 testi… 2021-0…

tximeta BiocFileCache

updated 4.7 years ago • judith.risse

<div class="preformatted">Sure. Maybe it's something that is clear to a biologist and I (as a physicist) cannot read in-between the lines. I redirected my question to a biologist at the Temple University whom we collaborate with. ... In fact I proposed to leave those miRNAs out of the validation table we are building. He disapproved. If he does not come up with the sequence then I will try …

PROcess PROcess

updated 15.6 years ago • mauede@alice.it

valule from fgsea is not truly significant as it is. When I search camera limma on pubmed, I found 2 papers. Thank you so much

fgsea GSVA CAMERA

updated 19 months ago • Chris

Hi, for the ones that created the tutorial "Chapter 24 Zeisel mouse brain (STRT-Seq) in single-cell" https://osca.bioconductor.org/zeisel-mouse-brain-strt-seq.html Could you tell me more about which methods you used to do "After sequencing, expression was quantified by counting the number of unique molecular identifiers (UMIs) mapped to each gene." We would like to analyze as a set of dat…

STRT-Seq single-cell tutorial

updated 5.5 years ago • tiphaine.martin

these results with RNA seq expression data results. Doing some research, I have come across many papers using p values but I am mainly interested in using variant data input. Any help would be greatly appreciated. Thanks

GSEA Variant Proportions Input

updated 10.3 years ago • manali.rupji

AH48041, an OrgDb for Ricinus communis from InParanoid. Today I'm writing Material and Methods for a paper on that analysis, and Annotation Hub was updated, and this object no longer exists... I'm a newcomer to Bioconductor, I didn

Orgdb

updated 9.0 years ago • anamabrantesc

<div class="preformatted">Hi, I've recently got some data from the lab coming from flow cytometry. I have the log10 values corresponding to the geometrical mean (not the flow cytometry files). Basically i would like to start from that matrix and compute the fold changes. I'm not sure which test is most suitable as not sure which sitribution the data follows , gaussian ??? could anybody sug…

updated 16.0 years ago • David

across all the samples. To do this I would appreciate if anyone can point me to similar analysis/papers done in the past or Bioconductor packages that could help out. I did look at limma but not sure if it is recommended for

limma microRNA limma microRNA

updated 11.9 years ago • Abhishek Pratap

Hello, Currenty, I call `` glmTreat `` method as following: tr <- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5)) topTags(tr) I discovered this [paper](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1006938#sec012) and In the "Differential gene...lt;- glmTreat(fit, contrast=B.LvsP, coef = 2, lfc=log2(1.5)) topTags(tr) I discovered thi…

edger

updated 8.2 years ago • mictadlo

code to produce results full sample data is needed, as our code is based on a pipeline included in a paper. I have tried to make a smaller dataset, however, the attempts have led to incomplete/inaccurate results. Is there a way

software error

updated 5.2 years ago • matt.moravec222

base level and considers the between sample variance? If yes, can anyone please reference me to the paper mentioning the same? Thanks Sahil

deseq2

updated 7.8 years ago • gupta

Axis. I have not been able to find this in the edgeR-manual or Mark Robinson's /Davis McCarthy's paper. Any ideas on this would be appreciated! Best, martin ______________________________________________________________________

RNASeq edgeR RNASeq edgeR

updated 14.9 years ago • Umhang, Martin

div class="preformatted">Hi to everybody, I've just red some days ago the new paper on "logit-t" method to analyze affy chips. -------------------------------------------------------------- "A high performance test of differential gene expression for oligonucleotide

Genetics Genetics

updated 22.2 years ago • Dario Greco

i'm not really convinced about the method that affymetrix provides (mas 5) so i read now many papers about how to normalize affymetrix chips. the method i like is the rma method from irizarry, but i do not know if we have

vsn vsn

updated 21.4 years ago • Dipl.-Ing. Johannes Rainer

CRAN: https://cran.rstudio.com/ Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Installing package(s) 'GenomeInfoDbData' installing the source package ‘GenomeInfoDbData’ trying URL 'https://bioconductor.org...installation of package ‘GenomeInfoDbData’ had non-zero exit status sessionInfo( ) R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running un…

GenomeInfoDbData

updated 4.6 years ago • ettore64

R-help, and post some problems > which I am facing. The Ref is a well known Genome Biology > paper "Bioconductor: open software development for > computational?biology and bioinformatics" by?Robert C > Gentleman...gt; featureNames instead > Hence I cant proceed to the next set of commands provided > in the paper which are as follows: > > ll …

Annotation GO Annotation GO

updated 14.5 years ago • Iain Gallagher

every morning 5 - 8 December 2006 * Keynote speakers on current research topics and contributed papers in the afternoon Travel Scholarships available: * for students (honours, master, PhD) and early career academics from...institution belongs to PRIMA Topics: * Monday: Introductory lectures in biology (no research papers) * Tuesday: Sequence to Structure * Wednesday: Comparative Genomics…

Cancer Cancer

updated 19.2 years ago • Sylvain FORET

Error in Prostar() : could not find function "Prostar" **sessionInfo( )** R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.3 LTS Matrix products: default BLAS: /usr/lib/x86_64

Prostar

updated 4.0 years ago • benoit.marchand

force = TRUE, intgroup = c("condition", "batch")) sessionInfo( ) R version 4.1.2 (2021-11-01) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19041) Matrix products: default locale

arrayQualityMetrics

updated 4.0 years ago • michael.s

Hi there, I have am getting different outputs after running enrichGO on cluster profiler when I put the same genes into enrichR (by Maayan Lab) website. Example here using Biological Process 2021 I have also tried other GO terms (Cellular Component and Molecular Funtion giving the same discordant results) Code should...I put the same genes into enrichR (by Maayan Lab) website. Example h…

enrichplot clusterProfiler

updated 3.8 years ago • angkoo

I am a biologist not a statistician. I have tried to understand the methods section of the DEseq2 paper, but unfortunately I still don't follow how to do this. For example, from my pilot dataset I have the mean expression and

DESeq2

updated 18 months ago • li.d.peck

loads fine. I will not be surprised at all :} if I am missing something obvious here. Am I merely papering over my ignorance by making that symlink? Thanks - - Paul </div

updated 19.6 years ago • Paul Shannon

done on the background corrected PM probes. Thanks. I did not find the details spelled out in the papers. Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814

Normalization probe Normalization probe

updated 19.9 years ago • Naomi Altman

Hi there, I am having some doubts about filtering low counts. I already read and read ... papers, questions in forums and i still have the same issue. I know that deseq2 has the independent filtering in the results

deseq2 noiseq lowcounts rnaseq

updated 5.2 years ago • andreia

Does anyone have any ideas? Also -- This is not the first time I have had a problem in producing a paper trail for an analysis and then reproducing it. How do other people handle this problem? rlm.output <- threestep(Dilution

ASSIGN ASSIGN

updated 21.6 years ago • Rob Dunne

testing correction. Is this implemented in Bioconductor at all? Having a quick glance at the paper it looks like it is related to Benjamin Hochberg but not quite the same. Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer

Cancer Cancer

updated 17.9 years ago • Daniel Brewer

which Published in Journal of Pulmonary Circulation of july-sept 2011 issue. In this research paper, researchers have mentioned that the open source software, R2.13/Biconductor 2.8 utilized for microarray analysis

Pathways Pathways

updated 11.8 years ago • Mayur Doke

<div class="preformatted">Hi, I am trying to create enrichment maps in HTSanalyzeR. I am fairly new to using R so I am using the paper X Wang et al. 2011 as a reference. When i get to the section on creating the enrichment map i keep getting the same error message...I am trying to create enrichment maps in HTSanalyzeR. I am fairly new to using R so I am using the paper X Wang et al. 2011 a…

HTSanalyzeR HTSanalyzeR

updated 13.9 years ago • Catherine Garry

website. Do I really need normal references for copy number/LOH analysis? Cheng Li of dChip had a paper in PLoS Computational Biology 2006 describing that dChip can infer LOH from unpaired tumor samples without using

affy affy

updated 15.0 years ago • array chip

Recently, I tried to follow the steps described in  "User instructions and tutorials of the _synergyfinder_ package", Authors: Liye He, Krister Wennerberg, Tero Aittokallio1, and Jing Tang, using data file called "mathews\_screening\_data" as an example. I succeeded to obtain the results at each step described in the paper mentioned above with this data file. My questi…

synergyfinder

updated 8.3 years ago • dimitriu.gabriel

Hello, I am having a hard time interpreting the IHW and Shrinkage method results. I have read the paper, and also vignette and other various other question threads. I understand the purpose of the methods, however, not sure...Hello, I am having a hard time interpreting the IHW and Shrinkage method results. I have read the paper, and also vignette and other various other question threads. I …

DESeq2 RNAseq

updated 19 months ago • kcarey

  __Background__ I'm currently trying to understand how RNA-seq analysis should be performed. I have read all manuals (+ the corresponding papers), however as I'm mostly concerned with bio-informatics regarding data cleaning and integration I find it hard to understand the statistics behind e.g. edgeR (If there are any recommendation (papers e.g.) to better understand these feel free …

R edgeR rnaseq rna-seq

updated 7.6 years ago • Mr.RB

When I run the MAGeCKFlute, the output graph and data are not based on my own data but the model data. For Example: > library('MAGeCKFlute') Loading required package: ggplot2 Loading required package: gridExtra Registered S3 method overwritten by 'enrichplot': method from fortify.enrichResult DOSE ###############################…

MAGeCKFlute

updated 6.1 years ago • pamelalee

<div class="preformatted"> Dear All: In the DEXSeq paper, the authors compared DEXSeq with Cuffdiff in terms of controlling Type-I error rates. From the mock comparison results (control vs. control), we can see DEXSeq reported far fewer genes with differential exon usage (DEU), as shown in Table S2 of the DEXSeq paper (2012). However, I think this kind of mock comparison is "under the null…

DEXSeq DEXSeq

updated 12.4 years ago • Guest User

dispersion parameter theta but having some problems. Any help highly appreciated.  __What the paper tells me__ In the DSS Bayesian hierarchical model, the biological variation among replicates of a group is captured...nbsp; __Good by cruel world__ I hope you can help me. I tried to get all the information from the paper <https://academic.oup.com/nar/article-looku…

DSS dmltest bayesian statistics methylation

updated 7.7 years ago • floriandeckert

how the FDR method is implemented at the level of "p.adjust" (package: stats). I have reread the paper by Benjamini and Hochberg (1995) and nowhere in their paper do they actually "adjust" p values; rather, they develop criteria

limma limma

updated 21.0 years ago • Kimpel, Mark W

CRAN: https://cran.rstudio.com/ Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.5 (2021-03-31) Installing package(s) 'DEP' trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/macosx/contrib/4.0/DEP_1.12.0.tgz...installation of package ‘bitops’ had non-zero exit status > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin17.0 (64-bit) Running…

DEP

updated 4.6 years ago • julie.hibbert

MT X Y 2507 1869 4364 1501 1630 1624 1404 1522 1865 985 1245 5232 2179 3997 2822 2524 3919 2021 2163 41 3297 17 R> table(getBM(attributes = c("ensembl_transcript_id", "chromosome_name", "strand", "transcript_start", "transcript_end...MT X Y 2507 1869 4364 1501 1630 1624 1404 1522 1865 985 1245 5232 2179 3997 2822 2524 3919 2021 2163 41 3297 17 R> sessionInfo(…

Annotation biomaRt Annotation biomaRt

updated 16.1 years ago • Ivanek, Robert

Hello, I am using Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10). I am handling a list of files received from Iscan machine, and I try to obtain the intensity of each bead, to my...Hello, I am using Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10). I am handling a list of files received from Iscan machine, and I try to obtain t…

IlluminaChip beadarray

updated 4.1 years ago • noa.gilat

that adjusting for multiple corrections may produce poor results, yet the authors of the above paper utilize a correction when producing their results. I also realize that GO is primarily for exploratory analysis, so

topGO Ontology DifferentialExpression

updated 3.2 years ago • Kevin Gregory

I am running GSVA on normalized RNA seq data. Is it acceptable to get all negative enrichment scores for a pathway? The heatmap below shows GSVA scores with pathways in rows and samples in columns. We note that some rows are all blue (i.e., enrichment scores for all samples for that pathway are negative). For those blue pathways, distributions of enrichment scores are unimodal and approx. symme…

GSVAdata GSVA

updated 3.8 years ago • random

to remove "potential dead cells - signified by high number of mitochondria). But have seen several papers where scater has been used to do something like the one I would want to do. I do not know how to do this. Some one who can help

SingleCellExperiment

updated 3.4 years ago • otieno43

104 sp0025270 0 0 0 0 and in this [paper](https://f1000research.com/articles/5-1438/v2) they added annotation with help > y <- DGEList(fc$counts, group=group) &gt

edger

updated 8.2 years ago • mictadlo

I want to extract differential expressed genes using LIMMA from RNA seq data for three cancer types viz breast, lung and prostate. These data should have tumor and normal samples. I have read some papers which have used data from TCGA. BUt now TCGA has linked to Genomics Data Commons and all data are not open access. All BAM...viz breast, lung and prostate. These data should have tumor and normal…

limma

updated 8.6 years ago • richa_makhijani

identify possible alternative splicing events. As I'm fresh in R and Bioconductor, any tutorials or papers i have found focused on human exon ST 1.0. Thus, i would like to ask if anyone has used the above genechip in R and how much

affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis

updated 10.8 years ago • svlachavas

I am trying to run and compare \`SCAN\` function of package \`SCAN.UPC\` , since in the paper the authors showed superior performance to RMA method. I have a cohort of Affymetrix HTA 2.0 arrays, save on my drive...I am trying to run and compare \`SCAN\` function of package \`SCAN.UPC\` , since in the paper the authors showed superior performance to RMA method. I have a cohort of Affymetrix HTA …

scan.upc

updated 8.1 years ago • Seymoo

Hi, I would like to check the definition of the data that INSPEcT labels as the 'total' RNA, as output by this function: ratesFirstGuess(nascentInspObj, 'total'). In the INSPEcT papers, generally the two populations of RNA are referenced as premRNA (P) and mature mRNA (M). Is the 'total' RNA level output by this...total' RNA, as output by this function: ratesFirstGuess(nascentInspObj, 'total')…

INSPEcT

updated 5.1 years ago • mkaythomp