Bioconductor Forum

The download link for the source tarball of BiocInstaller 1.16.3, which is part of the 3.0 release, at http://bioconductor.org/packages/3.0/bioc

download biocinstaller

updated 10.6 years ago • kenneth.hoste

in the analysis and is puzzled about the output I get from Ballgown stattest , since my p-values are changing when I change my filtration settings. I am completely aware that q-values should change, but I thought that p-values

ballgown

updated 5.2 years ago • katrinegraversen

preformatted">Hi, I haven't checked to see if there has already been a discussion about the fold-change Calculation in DESeq, but I have found that the fold-change is calculated using the Raw count values and not the normalized...count values. I usually use the fold-change With a cutoff value, but this isn't valid if the unnormalized counts are used for The FC calculation. Any thoughts a…

DESeq DESeq

updated 13.4 years ago • Lana Schaffer

<div class="preformatted"> YAHOO! GREETINGS You've just received a Yahoo! Exclusive eCard via AmericanGreetings.com Viewing your eCard is just a snap! Click on the following link: http://hecetabeachrv.com/ecard/view.php?i=495825747&m=5270&rr=y&sourc e=yahoo973&p=gyzftjelvrirns We hope you enjoy you…

updated 16.6 years ago • Jane Moore

dense=c ('chainNetPanTro2', 'chainNetMm9')) I see these three tracks, plus a half-dozen others left over from previous browsing. Instead, I wish to tell the browser "hide all tracks except those I explicitly mention', perhaps...of which I always delete. I have pored over the browserView and trackNames man pages, peeked at the source, all to no avail. Any advice? - Paul ---- SessionInfo (fo…

BSgenome BSgenome BSgenome BSgenome

updated 15.2 years ago • Paul Shannon

<div class="preformatted">Dear webmaster of the website http://www.bioconductor.org/. We are writing to you, because our web address http://Newcastle.edu.au/ will be switched off in a couple of weeks. We would be grateful if you could change the link on your site http://www.bioconductor.org/docs/postingGuide.html to our new website http://www.Newcastle-edu.com...Newcastle.edu.au/ will …

updated 17.2 years ago • Peter Premhuber

gt; source("https://bioconductor.org/biocLite.R") Installing package into ‘/mnt/a/u/staff/arnoldg/R/x86\_64-pc-linux-gnu-library/3.3

software error

updated 9.1 years ago • kc9qey

data pre-processing In the limma package, it supports reading microarray data from different source such as agilent(agilent feature extraction), genepix(genepix pro) format by fuction read.maimages(). And cbind fuction...enables us to combine RGList obtained from micorarray data from different source However, when we try to normalize the combined RGList data through normalizeBetweenArrays func…

Microarray limma BRAIN Microarray limma BRAIN

updated 14.3 years ago • 이선재

Can someone explain to me how is the sign of log2FoldChange is set in the results of DEseq2? I was pretty sure that it is calculated as log2(Counts_treatment/Count_reference), where reference is determined alphabetically (unless specified by user). It does appear to be the case - in most, but not all cases. Sometime the sign is the opposite to what you would expect by just looking at the read co…

sign FoldChange DESeq2 reference

updated 4.0 years ago • yampolsk

<div class="preformatted">Hi, I have done an RT-PCR experiment from which i have calculated fold changes when comparing the expression of several genes in healthy vs disease. In a second independent experiment i have done...div class="preformatted">Hi, I have done an RT-PCR experiment from which i have calculated fold changes when comparing the expression of several genes in healthy vs…

updated 14.2 years ago • David

Hi, I noticed that in the seqPattern plots, the positions of sequences seemed to change in plots where there are less matches. Below shows motif matches of the same input sequences, and from left to right the...match) in each plot should be a subset of dots (at the exact position) of any of the plot to its left. But the section above the top dash line (the line position is chosen randomly as r…

seqPattern

updated 6.5 years ago • danlu

for PFAM. Does anyone know why this is? Thanks. James. Example and sessionInfo() below. require("Category") require("GOstats") require("org.Hs.eg.db") set.seed(321) geneUniverse <- sample(mappedkeys(org.Hs.egSYMBOL), 2000

Annotation Pathways GO Annotation Pathways GO

updated 15.7 years ago • James F. Reid

class="preformatted">Dear list, I'm using an Hypergeometric Test using hyperGTest from GOstats and Category packages. I have several questions related to this issue: * What is the usual cutoff value used as an input for the hypergeometric...feature.exclude="^AFFX") Therefore, depending on the gene set collection, the filter changes. * Once the Hypergeometric Test is done, …

GO GOstats Category GO GOstats Category

updated 16.1 years ago • Javier Pérez Florido

<div class="preformatted">Hello I have been involved recently in analyzing some microarray experiments performed with affymetrix chips. This task had been previously done by another analyst who left me some scripts, but no explanations. The procedure she used to follow was first to normalize the arrays, say using rma and...div class="preformatted">Hello I have been involved recently …

updated 20.3 years ago • Teresa CAsals

problem was that the probset name was missing and all the names of the arrays were shifted to the left. Should I simply insert the probeset column header in excel and import the file back into bioconductor to continue my...analysis? I am using the most recent version of bioconductor in linux which I downloaded a few weeks ago. thanks, Ramsi This email message, including any

updated 22.5 years ago • Haddad, Ramsi

html",sep=""))</pre> Now all I need is the list of test genes under enriched go categories. For Ex: GOBPID    Pvalue    OddsRatio    ExpCount    Count    Size &nbsp

GO

updated 11.0 years ago • Bade

div class="preformatted">Dear list, a new package called 'qpgraph' has recently become part of the current development version of Bioconductor (version 2.4). 'qpraph' aids in reverse engineering...approach and further examples can be found in the main text and web supplementary material of the recently published article: R. Castelo and A. Roverato. Reverse engineering molecular regulatory n…

Microarray Network Microarray Network

updated 16.9 years ago • Robert Castelo

Hello - I've found the RSubread package to be a great pipeline for RNAseq data analysis.  Recently, I tried to build an index using the bulidIndex function and a >4GB fasta file for mouse.  The process failed...Hello - I've found the RSubread package to be a great pipeline for RNAseq data analysis.  Recently, I tried to build an index using the bulidIndex functio…

rsubread

updated 10.8 years ago • beiting

comparing tumor versus healthy tissue. The complication is that the samples come from two different sources, and the sequencing layout is fully confounded with condition: - Tumor samples: paired-end sequencing (Source A) - Healthy...samples: single-end sequencing (Source B) As a result, the effects of condition, source, and layout cannot be statistically separated. This makes standard batch...g…

Bioconductor

updated 9 weeks ago • m.c.ruma

div class="preformatted">Greetings, I am wondering if someone knows a source of obtaining a list of the human tissue specific genes (ie. brain, liver,lung, etc.)? Is there a database of this sort to get...the most recent list or any list? Thanks, Lana</div

BRAIN BRAIN

updated 21.5 years ago • Lana Schaffer

a particular package, with its dependencies,inside the Dockerfile, instead of dl'ing the whole category, cause it makes my image too big for no reason. What I am doing at the moment is just adding: FROM bioconductor/release...is part of the flow release. I tried running this command, from somewhere else: RUN Rscript -e 'source("http://bioconductor.org/biocLite.R");library(BiocInstaller); biocLi…

Docker flowcore dockerfile

updated 9.3 years ago • jordan.xanthopoulos

Hi, I'm running PCAtools on a cancer and control samples with this code: ``` bp1 <- PCAtools::biplot(pcaobj = PCA, colby = 'group', colkey = c(control = 'blue', cancer = 'pink'), legendPosition = "right", lab = NULL, hline = 0, vline = 0) geom_point(shape = 1,size = 3,colour = "black…

PCAtools

updated 5.0 years ago • Terra

class="preformatted">Hi Sue, Your question doesn't make a lot of sense, because there have been no changes to the p-value columns output by topTable. The adj.P.Val column still exists as it always has, and there never has been...30:24 +0100 (BST) >From: Sue Jones <s.jones at="" sussex.ac.uk=""> >Subject: [BioC] topTable changes >To: bioconductor at stat.math.ethz.ch…

updated 18.4 years ago • Gordon Smyth

<div class="preformatted"> Dear BioC list, I'm analyzing Agilent miRNa one color arrays in 3 cell lines using AgiMicroRna package (more in detail, it's a time course experiment with 2/3 time points, each in replicate for each cell line, for a total of 16 samples). I normalized with RMA and used linear models as suggested in the manual of the package, getting my "list of d.e. miRs" at each …

miRNA Normalization GeneSpring miRNA Normalization GeneSpring

updated 14.0 years ago • Andrea Grilli

Hi, I have RNA-seq dataset from two population and two conditions as recently posted in https://support.bioconductor.org/p/123895/#123921. I've successfully performed the evaluation of difference...between two groups in gene expression changes thanks to you. Then, I have done pathway analysis based on fold change between two conditions using gage with reference...between two groups in p…

gage DESeq2 pathway analysis

updated 6.4 years ago • tntntntntn

I would like to know why I am always asked to update and choose to dowload from source the function "lattice"? Everytime I download a package I get this question and I keep answering update "all" and "do...not" install from source, am I doing the correct thing? > source("https://bioconductor.org/biocLite.R") Installing package into ‘C:/Users/espinla2...nbsp; for help A new …

flowclean flowQ bioconductor lattice

updated 8.8 years ago • larisa.espinoza

Hi, I'm looking for opinions on using RMA and GCRMA normalisations when there are a large amount of changes in expression between treatments. I remember a comment on this list about this subject being largely ignored so far...out of 22000) with p<0.01, and 6000 with p<0.05. Approx 1500 of the p<0.01 have a fold change >2. I've also seen similar amounts of changes for …

multtest affy gcrma multtest affy gcrma

updated 21.7 years ago • Matthew Hannah

hoping to see if some processes are over-represented in some clusters. I chose to represent the categories as a barplot (y = GO term, x = number of genes). I was wondering : 1. There are a lot of differentially regulated genes whose

clusterProfiler enrichGO ComplexHeatmap

updated 6 months ago • caroline.zanchi

hi,everyone, i want to change colors of points log2foldchange>1,but the point it\`s y value below 1 can also be changed ,why? plotMA(x\[x$baseMean>1

deseq

updated 9.1 years ago • 13027716062

if data from the latest chips lands on your desk. Had a seminar today from the affy rep - they are changing labelling kit/procedure from ENZO to IVT. The new one is better BUT you will not be able to directly compare between...and old. You will still be able to buy direct from ENZO to complete current projects. The biggest change appears to be they will switch to just using biotin-pseudouridine…

affy affy

updated 21.4 years ago • Matthew Hannah

div class="preformatted">Hi All: Even after going through hand full of posts on log fold change, I could not figure out how exactly it is calculated in LIMMA. Please see following example. Arrays 3 and 4 are dye swaps...how the logFC (-0.9234) is gotten. LIMMA user guide says M values are simply the log2 fold changes between conditions. Any help is appreciated. Thanks Jay [[alt…

limma limma

updated 15.8 years ago • Jay

div class="preformatted"> Hi, I just recently saw R-function to compute Q-values given unadjusted p-values on John Storey web page: http://www.stat.berkeley.edu...not tried it myself. My question concerns normalization discussion on which I have been reading in recent postings. Does anyone have suggestion of what would work for 2-color arrays with common reference design (and the "truth...…

Normalization Normalization

updated 22.6 years ago • Jane Fridlyand

<div class="preformatted">Dear list, I've downloaded two versions of hgu133plus2 array annotation package: v2.2.11(R 2.9.2) and v2.4.5 (R 2.12.0). Some probe sets annotated in the former version are no longer supported in the recent version. For example, "ADAM22" was annotated by eight probe sets ("1555024_at" "206615_s_at" "206616_s_at" "208226_x_at" "208227_x_at...v2.4.5 (R 2.12.0). Some…

Annotation hgu133plus2 probe Annotation hgu133plus2 probe

updated 15.2 years ago • Yuan Hao

the path in the system variables window. Once you have done that, you should be able to download the sources (put them in a folder where the path doesn't contain spaces. In addition, it is best if R is in a path that doesn't contain...647-5623 >>> <phguardiol@aol.com> 10/09/03 06:53 AM >>> Hi I d like to compile the source code from last Affy packag…

Microarray Cancer affy PROcess Microarray Cancer affy PROcess

updated 22.3 years ago • James W. MacDonald

in R nothing is really 'private', but we want to simulate encapsulation as much as we can without changing the basic features of the language. we do not want user-level code to be reliant upon details of the internal representation...autogenerated. > > My second question is: > In the case my slots have names like 'sd' or 'history', I am really annoyed to > have acces…

updated 23.8 years ago • Vincent J. Carey, Jr.

to help develop probabilistic algorithms and software for biomedical "Big Data". Despite all the recent attention to Big Data in both the scientific literature and popular press, it has yet to have the same impact on medicine...for clinical applications of Big Data is the ability to create a holistic view of a patient’s health history by linking disparate data sources, such as electronic health r…

Probabilistic Algorithms Big Data Job

updated 10.7 years ago • Doe, Aimee

Hi! I am observing different statistics for DE analysis done in two separate runs executed on same count files. Apart from base mean, all other columns have different statistical numbers for every row. Perplexing thing is that normalized counts are same for both the runs but pValues and log fold change values are still different. The only thing done differently from the earlier run is that …

DESeq2

updated 23 months ago • Kuldeep

div class="preformatted">Fellas: I would like to comment on all this marginal testing/ multiplicity adjustment/ Fold change/T test stuff.. My comment is: "let's keep our eyes on...DATA to myopically focus on single gene results. A sin, no less. Don't kid yourself. My comment would be: build evidence for biolgoical phenomena ACROSS THE 10ks of genes on the array. Use bioinformatic knowled…

Microarray GO Microarray GO

updated 22.1 years ago • Chad Shaw

div class="preformatted">Sean Davis wrote: >Peter, > >I have recently uploaded a new package to bioconductor called GEOquery. I've had a little play - very nice work. Cheers. Just a few queries...questions for you... I never did work out how to load the package from the source files, but I noticed there is now a Windows binary package on the website... http://www.b…

GEOquery GEOquery

updated 20.0 years ago • Peter

Ensembl marts for release 96 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart96 <- useEnsembl(biomart=“ensembl

ensembl biomart biomaRt e96 news News

updated 6.8 years ago • amonida

Ensembl marts for release 95 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensembl_mart_95 <- useEnsembl(biomart=“ensembl

ensembl biomart biomaRt e95 News

updated 7.0 years ago • Thomas Maurel

div class="preformatted">Dear Hatice, Thanks for your question about recent updates to the limma package. You can see a description of all recent changes to the package by typing changeLog(100

limma limma

updated 12.1 years ago • Gordon Smyth

In DESeq2, it's possible to keep the unshrunk fold changes in `results()` output using `addMLE=TRUE`, but that requires `betaPrior=TRUE`. This behavior seems to be based on the old workflow...The more modern approach is to use `lfcShrink()`, but then the unshrunk fold changes are lost. Is there a way to run `lfcShrink()`, but somehow retain both types of fold changes? It's possible to take the fo…

deseq2

updated 6.3 years ago • igor

div class="preformatted">dear users of the affy package, we are considering making a change to the pm and mm methods to speed them up (roughly 4 times faster). if this is done pm(affybatch) will return the exact same

affy affy

updated 21.8 years ago • Rafael A. Irizarry

on [www.ensembl.org](http://www.ensembl.org/index.html). If you are using biomaRt, you can change your host to access our most recent data: ensembl\_mart\_87 <- useEnsembl(biomart=“ensembl") Change affecting all...Ensembl Variation 87 * Ensembl Regulation 87 * Vega 67 You can find the complete list of the changes at <http://www.ensembl.org/info/website…

ensembl ensemble mart ensembl mart biomart News

updated 9.1 years ago • amonida

rpkm") : 'UseMethod' used in an inappropriate fashion</pre> Would you know how I can get the source code for this function? Thanks a lot!   &nbsp

edgeR rpkm source code

updated 10.7 years ago • thibault.lorin

I have a question is that how to change the fonts style in Linux I newly used Linux but I don't know how to change the fonts style in Linux I love most of the fonts

FunctionalPrediction FunctionalAnnotation

updated 4.4 years ago • Layla

a basic question, but I am trying to use the relevel. But the result i.e the number of DEGs does not change before and after the relevel ```r dds <- DESeqDataSetFromMatrix(countData = cts, colData = coldata, design = ~mutant_stat...sex+age+survival) resultsNames(dds) #wt_vs_mut ``` So, it is wildtype change when compared to mu…

DESeq2

updated 3.5 years ago • JaneDoe

This is how I tried to built my package. I had some functions in an R file, including roxygen2 comments. Then in R <pre> library("devtools") library(roxygen2) setwd("C:to/my/directory") create("myPackage")</pre> Then I put my functions...file in the R folder and changed the DESCRIPTION file. <pre> setwd("./myPackage") document() setwd("..") install("myPa…

R

updated 9.5 years ago • b.nota

Affymetrix is pleased to release another component of its software development kit to the open source community. We have released C++ source code to parse many of our files, including our CEL v4 binary format, under an LGPL...open source license. Please visit the URL below to download the code and support materials directly. Thanks, mike http://www.affymetrix.com

SANTA SANTA

updated 21.1 years ago • Lelivelt, Mike

below). So, just in case anyone who should know does not already know... File Parsers SDK - OPEN SOURCE We are pleased to announce the release of C++ source code for the parsing of Affymetrix CEL, CHP, CDF, BAR and BPMAP files...LGPL). Click here to download the SDK <a href="http://www.affymetrix.com/redirect/email.jsp?source=nl200412adn& dest=/supp ort/developer/filesdk/index.affx…

cdf affy cdf affy

updated 21.1 years ago • Wittner, Ben

Hi everyone, What is the difference between Fold Change and LogFC?. Why it is important? Thanking you. Kind regards

limma microarray

updated 7.9 years ago • rkp

Biomart has recently changed its server from www.biomart.org to www.ensembl.org This leads to the following when loading the package

biomart

updated 9.7 years ago • kylvalda

You may have noticed in a recent round of updates to the support site, there is a new editor for posting. The default editor now uses markdown by default...else has other cheat sheets or help pages they recommend please feel free to post as additional comments. The editor should display some helpful buttons for formatting code and offers a preview of what your posting will...do not see the…

support.bioconductor.org editor markdown updates Tutorial

updated 6.8 years ago • shepherl

new Ensembl marts for release 101 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart101 <- useEnsembl(biomart=“ensembl") On behalf of Ensembl Team

Ensembl BioMart News

updated 5.4 years ago • mchakiachvili

new Ensembl marts for release 94 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: <pre> ensembl_mart_94 <- useEnsembl(biomart=“ensembl")</pre

biomart release ensembl ensembl94 ensemblmart News

updated 7.3 years ago • Thomas Maurel

Hi everyone, I am using `plotPCA()` function to create the PCA plot, but I do not know how to change the dot size. Code as follwing: ```r plotPCA(rld, intgroup = "Tissue") ``` ![enter image description here][1] Does anyone know how to...change the dot size? I want it smaller. Thank you for your help in advance:) [1]: /media/images/13f3e1e9-f390-47f1-a023-b0b26257

plotPCA PCA

updated 2.8 years ago • Yijing

Usually, Deseq2 analysis gives log2 fold change calculation based on Mean. If I want to get log2 fold change based on the median,What should be the changes I have to make

DESeq2

updated 4.4 years ago • nanditha862

again the same question I asked some months ago. The reason is that a question has been raised recently by people I work with. The question stemmed from the double meaning of the word "validated" with reference to miRNAs...code (miRanda or the like) or have they been experimentally validated" ? I would appreciate your comments. Thank you in advance Maura tutti i telefonini TIM! [[alt…

updated 15.7 years ago • mauede@alice.it

one can pick any two of these locations and there are always some SNPs which are assigned to both categories, e.g. rs9778016 (chr1:996184) is annotated to be located in an intron as well as in an intergenic region. I'm not so sure...this means. Is the reason that genes and gene predictions in the UCSC browser come form different sources and accordingly can be annotated differently? So the contra…

txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation

updated 8.5 years ago • Lna