Bioconductor Forum

Hi, I am a Student currently trying to learn and to understand how to analyse microarray data with R and Bioconductor. I am following this course : I am currently in the second part, but I already noticed some problems when doing the following :

tab = topTable(data.fit.eb,coef=2,number=2000,adjust.method="BH")
topups = tab[tab[, "logFC"] > 1, ]
colnames(topups)
IDsup = topups$ID

The…

limma microarray tutorial

updated 9.8 years ago • giroudpaul

Hi All, i am using R and Bio conductor for analyzing TCGA controlled data BRCA.  data category raw microarray data type raw intensities platform Affymetrix SNP Array 6.0 access controlled i used commands...data is downloaded and placed in working directory   please help me.. i am not finding any source for help   Thank You regards ugandhar

R tcgabiolinks gdcprepare

updated 8.6 years ago • ugandhar.ch1

Hello everyone, How to change the FDR threshold in DESrq2? when we use summary function to find out number of up and down regulated genes, it gives...Hello everyone, How to change the FDR threshold in DESrq2? when we use summary function to find out number of up and down regulated genes, it gives values...at default FDR= 0.1 Even though I changed FDR into 0.05, still it shows as 0.1 wh…

DESeq2

updated 3.7 years ago • devi

two questions about this value. I. As far as I know, this is a moderated version, not a log2 fold change from the raw count value. But I want to have unmoderated value that can be calculated from count directly and my current...per condition (4) divide two averages: "FC". Is this a right way? I am confusing whether it is fold change of log, or log of fold change. II. Effect size is "log2Fo…

deseq2

updated 6.6 years ago • bioinfo

I successfully made a heatmap using dba.plotProfile and now understand a bit of profileplyr to change some aesthetics. What I couldn't understand were some details. 1. In one tissue (data set 1), the plot shows WT first on the...left and then the mutant on the right, and for the other tissue (data set 2), it's shown in the opposite (the mutant first, WT second...answer about this and use…

DiffBind

updated 3.1 years ago • Junsik

2006 11:09 Till: 'Lina Hultin-Rosenberg'; bioconductor at stat.math.ethz.ch ?mne: RE: [BioC] heatmap - changing title size Hello. I think if you set the par(cex.main=.8) prior to the heatmap call, the size of the title should change...Tuesday, September 12, 2006 10:25 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] heatmap - changing title size Hi all! I am using the heatmap method t…

updated 19.3 years ago • Lina Hultin-Rosenberg

In HTqPCR, the header in SDS files is identified as the first line beginning with a hash mark (\#). Newer SDS file formats use the word "Well" at the beginning of the header line instead. For that reason, HTqPCR fails to read recent SDS files. This can be solved easily by adding "Well" as one alternative when searching for the header in the SDS file. Also...the word "Well" at the beginning of the…

htqpcr

updated 8.9 years ago • henrik.seidel

span style="background-color:Yellow">Sequence features: [1] DB [2] AccessionNumber ... [10] Comment [11] Filename Peptide features: [1] DB [2] AccessionNumber ... [46] spectrumFile [47] databaseFile</span></pre>   Specifically...go to \[13\] and should include "npeps" and "ENST".  Peptide features should only have \[28\] categories, where you can see my l…

Pbase

updated 10.4 years ago • nic.bowman

readTargets("targets_genepix.txt") rg_agilent = read.maimages(targets_agilent$FileName, source="agilent") rg_genepix = read.maimages(targets_genepix$FileName, source="genepix") rg_all = cbind( rg_agilent, rg_genepix...at stat.math.ethz.ch > Subject: [BioC] [question] integration of microarray data from different sources in limma package > > Dear developers, > > …

Microarray limma BRAIN Microarray limma BRAIN

updated 14.3 years ago • 이선재

pre> In my dataset by h = 0.9, I can’t see any line in my “Scale independence” diagram but when I change h value to 0.8(h = 0.8) then I can see the red line in my diagram and also have intersect with one of my candidate value...for power. My question is that can I change h value from 0.9 to 0.8? If no, what should I do for solving problem? I appreciate if you share your comment wit…

wgcna abline function Scale independence diagram

updated 7.2 years ago • modarzi

Hi, Recently i've posted a couple of comments on `Biostars` web site: "Why we need to make a `GLM` model before performing a `Wald test` itself

deseq2

updated 6.6 years ago • s.apocarpum

of cells in an attempt to make immoralised cells. I need to work out which of these genes have changed expression and are transformed, but i am unsure how to do this as i havent been given any numerical information about...how different the expression it needs to be for it to count as 'changed'. I have tried using logs and ploting various graphs but i need to get some more exact info. any ideas?…

differential gene expression r commander

updated 9.8 years ago • milliesteward23

publications where Deseq2 is used for differential abundance analyses of 16s rRNA data. I've recently been informed that Deseq2 may not be appropriate for analysis of 16s reads. Can anyone provide the evidence-based...sources that explain why Deseq2 should not be used for microbiome data and provide any alternatives to hypothesis testing

Microbiome 16s Deseq2 16srRNA

updated 3.7 years ago • Katelyn

div class="preformatted">Hello, I recently update R to 3.1.0 and after I did the following, I saw the dexseq version of 1.9.**. But I cannot find an explicit sample...guide using this newest version. How can I go back to use the dexseq 1.8.0 version? source("http://bioconductor.org/biocLite.R") biocLite("DEXSeq") Thanks, Xiayu [[alternative HTML version deleted]] </div

GO DEXSeq GO DEXSeq

updated 11.7 years ago • Rao,Xiayu

I have a pathway plot using cnetplot() in R from the enrichplot package. I am able to change individual gene nodes' colors no problem, but I want to change the beige pathway nodes colors and I can't figure out how...The plot output essentially looks like any cnetplot with beige pathway nodes - how can I change the color of these nodes in particular? I've tried running this code but it doesn't …

cnetplot r enrichment

updated 3.9 years ago • DN1

Yes, British Airways allows flight changes, ( +44-144-631-8041 UK & +1(877) 777-5946 US ) but fees may apply depending on the fare type. Flexible tickets may be changed...for free, while standard fares may incur a change fee and fare difference. To modify your flight, visit the BA website or call British Airways at +44-144-631-8041 for assistance

org.Sc.sgd.db MafDb.1Kgenomes.phase1.GRCh38 ncdfFlow

updated 9 months ago • Haggu

Dear Sir, I am using package"ropls" to generate PCA Plot. I would like to change the labels name to symbol and change the font size of x- and y- axis. In addition, we would like to have the 2 ellipses of vector

software error

updated 6.6 years ago • laor.cha

Recently I read one of your paper titled with “FELLA: an R package to enrich metabolomics data”, and met a problem. I want to present...provided by the R package “FELLA”, but the graph can’t be drew with modification, for example, to change the color, shape and the distance between text and graph

software error FELLA

updated 7.0 years ago • jnzd_hemaozhang

MSAs generated by HMMer, generating the "alignment rows out of order" error. On looking through the source, I think the problem arises from read.MultipleAlignment.splitRows() not correctly handling alignments where each...row of the alignment can further be annotated by a comment line (e.g. "\#=GR ...").  alnlines in the existing code (line 304 in MultipleALignment.R in github) expects …

biostrings

updated 9.1 years ago • david.huen

All, I'm trying to compare two tables in R and find the differences between them (what has the user changed). The approach is the following: - Import .xls table into matrices - compare matrixes (and highlight differences) - output...in R pretty easily, but the people I'm working with need a .xls file in return, with the highlighted changes (for example fill the cells which have changed with a col…

updated 12.3 years ago • Patrick Schorderet

an RNA-seq experiment with 2 conditions and unfortunately no replicates. I probably don't have big changes in expression, 100-200 genes with logFC max 2-3. I'm planning to do the the following: 1. Salmon/Kallisto with a recent RefSeq...to estimate read counts. 2. tximport to import gene level counts with an offset that corrects for changes to the average transcript length across samples. 3.…

rnaseq deseq2 tximport

updated 9.1 years ago • Endre Sebestyen

Hi, I'm trying to measure RNA stability changes after knocking out a repressor RNA binding protein. I'm using 4sU to label nascent RNA and also collecting total RNA...RNA stability by the ratio of nascent RNA/total RNA. I'm using the interaction in limma to look at changes in RNA stability between WT and KO cells. The issue that I have run into is that it looks like some genes are stabilized...h…

limma voom rnaseq

updated 7.9 years ago • Jake

I use the  "AnnotationHub(), query(hub,'zea') " function to get the results shown in the left, but I get the result is the right look, the lack of 'AH55736' is exactly what I want. ![](http://img.blog.csdn.net/20170811091923787...Then I try to change the "snapshotDate()" date, but still do not get the desired result. As follow: ![](http://img.blog.csdn.net/20170810191640350

orgdb annotationhub

updated 8.4 years ago • slbai01

and an error about needing to use 3.2.2. I am running this on Windows XP SP 3 32 bit.   > source("https://bioconductor.org/biocLite.R") Error in file(filename, "r", encoding = encoding) :    cannot open the connection...encoding) :   InternetOpenUrl failed: 'The connection with the server was reset' > source("http://bioconductor.org…

spade

updated 10.2 years ago • frostbite907

div class="preformatted">Hi Lavinia, One reason we changed the default normalization method as quantile is that quantile is more popular method and seems more robust for...gt; > Many thanks for the prompt reply to my email, that is greatly appreciated. > As you have changed the default normalization, is this because you now feel > that quantile is more appropriate, or is …

Normalization probe lumi Normalization probe lumi

updated 17.5 years ago • Pan Du

no data loaded it works fine with sample data set 'eset', therefore, it clearly needs to some how change my data format. My data format is probe exp1 exp2 ... 1037_at 23 34 ... any comments? Thanks. Zeren Gao</div

genefilter genefilter

updated 22.7 years ago • ZRG Zeren Gao

Seems relatively basic, but I can't find a way to change graph dynamics using the `plotExpression()` function in `scater`. For example, I have the following gene expression plot...Specifically, I want to be able to do the following: 1. Decrease point size 2. Create and change point borders 3. Change transparency of points 4. Change legend title In general, within `plotExpression()` a…

scater plotexpression singlecellexperiment plotting

updated 6.7 years ago • kushshah

not much difference between replicates). 80 / 990 = 0.08 so doesn't that mean that the Log2 fold change should be approximately -3.64 in treatment 1? I am getting a Log2 fold change of only -0.75, which seems way way off. What

DESeq2 TPM Foldchange

updated 3.8 years ago • dadca596

had done that treatment). =20 I hope my question is clear and would very much appreciate your comments = on this. Regards Larry Heisler Dept of Laboratory Medicine and Pathobiology Program in Proteomics and Pathobiology...color:='transparent"=20' border-bottom:="" border-left:="#c0c0c0;" border-top:="" style='3D"BORDER-RIGHT:' width="3D64" width:=""><font face="3DArial" size="3D2">3chi…

Proteomics affy PROcess Proteomics affy PROcess

updated 23.5 years ago • Larry

outcomes or markers, I would not perform filtering in correlation with any of these indices. A recent paper in PNAS on class discovery of tumor tissue subtypes (spot cDNA arrays) used the following strategy for filtering...intensities below 150 are unreliable and indicative of merely a low value (derived from a couple of sources) - I would aim towards filtering in genes with at least 2 samples w…

affy affy

updated 21.8 years ago • Tan, MinHan

that it can be put back to the development branch (2.8) as soon as possible. Meanwhile, we will change the maintainer's email address. Thanks for noticing the defunct address. I will get back to you as soon as the package...Sent: Monday, January 31, 2011 12:08:11 PM Subject: [BioC] iFlow and current Bioconductor release I recently tried to install the iFlow flow cytometry GUI on top of my R/Bio…

GUI Cancer iFlow GUI Cancer iFlow

updated 14.9 years ago • Chao-Jen Wong

for each probeset. I now want to do the comparison between two classes of the samples (i.e. fold change between the classes). One thing I'm not sure is how to compare them because, as I read from the gcrma paper, the expression...the expression values from gcrma() back to raw values by e^(values) before calculate the fold change between the two classes that I have? Best Yot </div

gcrma convert gcrma convert

updated 14.6 years ago • yotsawat pomyen

<div class="preformatted"> Dear list, I have a few gene lists derived from a human Illumina expression array. I just have Illumina IDs, I have gene names, and I have entrez gene IDs I obtained for them. I would like to analyse the list to look for over-representation of some category, probably using gene ontologies. I see there are several packages that seem to address this, although when…

affy Category nudge affy Category nudge

updated 15.9 years ago • J.delasHeras@ed.ac.uk

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\_86 <- useEnsembl(biomart=“ensembl") * Ensembl Genes 86 * Mouse...Ensembl Variation 86 * Ensembl Regulation 86 * Vega 66 A complete list of the changes in release 86 can be found at <http://www.en…

ensembl biomart ensembl release ensembl mart News

updated 9.3 years ago • Thomas Maurel

Inf and p.value=0.05 to get all significant genes for a given condition, regardless of their fold change. I seem to be getting significant genes with a fold change systematically bigger than 1.3 (linear scale), both up and downregulated...in the analysis. I guess I expected that some genes would be significant even with a very small fold change. I tried the same analysis with the ALL dataset and …

Microarray vsn limma Microarray vsn limma

updated 15.2 years ago • Eva Benito Garagorri

Hello, I'd like to know how the log2 fold change is calculated between target and comparison population in DEXSeq. Going over the **estimateExonFoldChanges** function...Hello, I'd like to know how the log2 fold change is calculated between target and comparison population in DEXSeq. Going over the **estimateExonFoldChanges** function in an older version (0.12.1) of the package, I realize th…

DEXSeq log2foldchange Tutorial

updated 5.8 years ago • tmvarsha

Thank you. Someone had already suggested TarBase. Maybe you did. Since these files are often changed ... at least they should be .... we would like to implement a procedure that download such files and process them as automatically...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 …

PROcess PROcess

updated 15.7 years ago • mauede@alice.it

that DESeq2 can work for the data, however why are there some gene-est which are at the lower left corner? Is it because they have too little reads? I have filtered the data as mentioned in the documentation. Also, the plotMA...for res and resLFC seem to have very few blue points (i.e. significant fold change right?). How can I interpret this? That there are very few log fold changes with high…

RNASeq DESeq2

updated 2.2 years ago • Karthik

I am very new to all of this. I have a problem with the output of goseq. I get many GO terms in each category instead of getting one go term per category which is what I see in every paper. I believe that it might have something...BH") \#add adjusted p-values  enr <- subset(k, k$bh\_adjust < 0.05) \#get enriched GO categories enr: <table border="0" cellpadding="0" cel…

go goseq goterm category

updated 7.4 years ago • Juan

Checking R Version dependency... * Checking package size... * ERROR: Package Source tarball exceeds Bioconductor size requirement. Package Size: 8.6382 MB Size Requirement: 4.0000 MB * Checking individual...Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity..…

package development

updated 7.3 years ago • ntueeb05howard

Hello, Would it be possible to modify _makeOrgPackage_ to allow for GO that are not currently in the most recent GO.db? I would be happy to submit a pull request with the functionality, if you think it is reasonable to include, but wanted...be possible to modify _makeOrgPackage_ to allow for GO that are not currently in the most recent GO.db? I would be happ…

annotationforge makeorgpackage go

updated 10.6 years ago • Keith Hughitt

div class="preformatted">Dear list, Is it possible to change the default ACGT to ACGU in seqlogo? I see there is a line in seqlogo, but I cannot change it. chars <- c("A", "C", "G", "T") </div

seqLogo seqLogo

updated 12.1 years ago • Fabrice Tourre

<div class="preformatted">Hi I think I am probably being a complete idiot, but I can't change the fontsize in simple Rgraphviz plots: library("Rgraphviz") set.seed(123) V <- letters[1:10] M <- 1:4 g1 <- randomGraph(V, M...div class="preformatted">Hi I think I am probably being a complete idiot, but I can't change the fontsize in simple Rgraphviz plots: library("R…

Rgraphviz Rgraphviz

updated 17.3 years ago • michael watson IAH-C

HTqPCR would still work correctly even for those older Bioconductor versions. Here are the source code locations which need to be changed: <pre> qPCRset.R:32: function (object, value) assayDataElementReplace(object

HTqPCR

updated 9.0 years ago • henrik.seidel

genome array results). The obvious analysis problems with a focused array where most genes are changing are: 1. LOESS normalization assumes most genes are not changing. If most of the genes are expected to change, there is...no basis to recenter the data around zero. The response from the lab was that they would be willing to include 100-150 genes that are not...expected to change. 2. The B-…

Normalization limma Normalization limma

updated 20.6 years ago • Mike Schaffer

div class="preformatted">Dear all, I have a problem with the log Fold changes calculated in Limma. I am using protein abundance index of proteomic data The log2 of this data is normally distributed...1, adjust="BH") Taking one gene as an example. NAMPT in tumour versus wound and calculating fold change by hand of normalized data; > norm_ctw["NAMPT",] cam1 cam2 cam3 tumour…

limma limma

updated 13.5 years ago • john herbert

div class="preformatted">As of the very latest version of getBioC (1.2.23) there is a small API change that is unlikely to affect many users, but for those who it might affect ... Previously the version 'force' was defined as

reposTools reposTools

updated 22.8 years ago • Jeff Gentry

Hello, I was hoping someone may be able to help me with interpretation of Log2Fold change and its specific interpretation when used with a continuous predictor variable. I understand that the Log2Fold...change when used with a predictor variable should be interpreted as change per unit of the variable. However, my question is...variable I am finding that my results are significant (adjust…

DESeq2

updated 2.9 years ago • m.c.stanley

I just tried AffylmGUI with R2.15.2 on a Windows 7 Enterprise machine with service pack 1 and recent updates. I found that when I am at the point at which the target file is read in, I cannot type the name of the targets file

Cancer affylmGUI Cancer affylmGUI

updated 13.0 years ago • Richard Friedman

new Ensembl marts for release 103 are now live on www.ensembl.org. If you are using biomaRt, you can change your host to access our most recent data: ensemblmart103 <- useEnsembl(biomart=“ensembl") PS: if you want force one previous

biomaRt ensembldb Ensembl ensemblVEP Biomart

updated 4.7 years ago • mchakiachvili

the amino acid for TAG/UAG. Is there a way to edit the standard genetic code table in Biostrings to change TAG from a stop codon to X? Thank you, Sam

Biostrings

updated 3.9 years ago • Sam

the google form several times to submit my github ID, waited some days and then tried to fetch the source from git@git.bioconductor.org:packages/oposSOM.git  which results in the error message "Permission denied

git github developers

updated 8.0 years ago • wirth

end result, the font on the labeling for each track seem too big, e.g. 'genes', 'H1', 'H2'. I can change these after exporting to PDF and edit by AI. But, is there a way to change font size in R code? Thanks! ![enter image description...lt;- optSty$style setTrackViewerStyleParam(viewerStyle, "margin", c(.05, .2, .05, .05)) #bottom, left, top and right margin. setTrackXscaleParam(trackLi…

trackViewer

updated 4.2 years ago • liruiradiant

Hello, I just want to clarify this questions: What relationship exists between the Fold Change and SLR? How can I express the SLR change with respect to the Fold? Thanks for the help!!! Laura [[alternative HTML version

updated 13.9 years ago • Laura Bermúdez

I am new to Bioconductors and I am trying to read some set of CEL files using Oligo package in R: source("https://bioconductor.org/biocLite.R") biocLite("oligo") biocLite("pd.hta.2.0") library(oligo) library(pd.hta.2.0) celFiles...w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 and  > source("https://bioconductor.org/biocLite.R") …

oligo pd.hta.2.0 CEL R windows 7

updated 8.4 years ago • ladhikari

new Ensembl marts for release 91 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_91 <- useEnsembl(biomart=“ensembl")</pre>   Ensembl Genes..._feature" to "hsapiens\_peak" and "mmusculus\_peak"   You can find the complete list of the changes at <http://www.…

ensembl biomart release ensembl91 News

updated 8.1 years ago • amonida

<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...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...the flow cytometry files). Basically i would like to start from that …

updated 16.1 years ago • David

div class="preformatted">The limma change log is no longer linked to from the URL http://bioinf.wehi.edu.au/limma but instead is distributed as part of the package

limma limma

updated 21.4 years ago • Gordon Smyth

In the process of validating my procedure for using edgeR to calculate differential expression statistics; I've found that there are differences between the fold changes estimated by glmLRTest, and those calculated directly from the matrix of scaled cpm values returned by "cpm(y)". I am aware...calculate differential expression statistics; I've found that there are differences between the fold c…

edger RNA Seq

updated 6.1 years ago • abf

I have a set of genes meeting my cutoff for significance along with their associated log2 fold changes. My question is what do the log2 fold changes represent in a 2 x 4 interaction? I understand from a previous post (https...support.bioconductor.org/p/60543/) that I can think of the log2 fold change in a 2 x 2 interaction as a ratio of ratios, and this makes sense to me, but I am not sure how to…

deseq2

updated 5.8 years ago • julia.chariker