Bioconductor Forum

<div class="preformatted">Dear Alessio and Gavin, Thanks for pointing out the problem with reading quantarray files. The bug has now been fixed in limma 2.9.1. limma now reads the annotation columns for quantarray files as well. Best wishes Gordon > Date: Wed, 4 Oct 2006 09:43:50 +0100 > From: "Gavin Kelly" <gavin.kelly at="" cancer.org.uk=""> > Subject: Re: […

Annotation Cancer limma Annotation Cancer limma

updated 18.9 years ago • Gordon Smyth

<div class="preformatted">I'm not sure if this is the best place to address this question, but not sure where else to turn: I've been exploring RStudio using the Bioconductor ami, ami-b5a079dc, and running a micro instance (this has Bioconductor 2.10 and R 2.15 in the instance). I've been able to run RStudio. However, I can't change into a different directory, e.g. setwd('/root'), that i…

updated 13.4 years ago • Andrew Yee

dockerimages/#setting-tags-on-an-image)) years later and know that nothing in the container has changed.  * _ease of use_: With one command, you can be running the latest release or devel Bioconductor. No need to worry about...see our [Docker Containers](http://bioconductor.org/help/docker/) page. Let us know if you have comments or questions. <span style="line-height:1.6">Dan&l…

docker News

updated 10.7 years ago • Dan Tenenbaum

t-34614.html, post by simon anders, 10-21-2013, 12:28 AM). So in the example above, the fold change would be calculated for each patients, and the test made on these fold changes, I am wrong? Is it possible to get the individual...fold change for each patients? Thanks, Samuel </numeric></factor></factor></factor></character></div

DESeq2 DESeq2

updated 11.3 years ago • samuel collombet

identify genes with genotype:condition interactions. The res objet report p-values but also log fold change. How can I make sense of these fold changes?  At least how can interpretive negative from positives log fc?   I will

deseq2 logfoldchange interactions

updated 9.5 years ago • colaneri

However there are no replicates; only one case and one control. I want to plot how the Log2 Fold change is correlated between the two data sets as they are looking at similar samples. The microarray data is easy as Limma...reports log2 fold change but NGS on the other hand does not. What would be the best package/approach to generating a log2 fold change of the next

RNASeq Microarray limma RNASeq Microarray limma

updated 14.2 years ago • john herbert

I have followed the Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification vignette to analyze my data and had no problems. Specifically, I used DEXseq followed by stageR. However, I was hoping to get fold changes for individual transcripts that show evidence for DTU. The only output I get are the pvalues for each transcript. Is...had no problem…

DEXSeq stageR

updated 22 months ago • jbono

and it seems that packages can be updated just by pushing to the master branch with a version change. So, is it sufficient for us to have admin rights to the repository? Any other steps that need to be taken? &nbsp

developers bioc-devel

updated 8.4 years ago • mlbendall

Hi,  (I've asked a lot of questions about limma over the past week so I'm hoping this'll be the last for a while!) Given the following details: <pre> expression_data <- c(1.27135202935009, 1.41816160331787, 1.2572772420417, 1.70943398046296, 1.30290218641586, 0.632660015122616, 1.73084258791384, 0.863826352944684, 0.62481665344628, 0.356064235030147, 1.31542028558644, 0.…

Limma

updated 10.2 years ago • andrew.j.skelton73

Hi, Can we change the name of the ColAttributes in the image generated by dba.plotHeatmap? As I have two attributes in my data `DBA_CONDITION

DiffBind plot plotHeatmap dba.plotHeatmap

updated 6.0 years ago • researcher

in each of the conditions.. I wanted to confirm my results before publishing and re run the code recently. Everything is the same except 3 pathways do not come up anymore ( estrogen receptor pathway and two eicosanoid metabolism...Which leads me to think that it is not they are not significant but something in the package perhaps changed? If I use the online tool Webgestalt and the same exact…

clusterProfiler

updated 3.1 years ago • Susana

div class="preformatted">Hi all, Were there recent changes in GenomicRanges that might cause this? R> class(sortedBloodCells) [1] "SummarizedExperiment" attr(,"package

GenomicRanges GenomicRanges

updated 12.6 years ago • Tim Triche

new Ensembl marts for release 89 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_89 <- useEnsembl(biomart=“ensembl")</pre>   Ensembl Genes...and mouse Please note that the vega mart has been retired. You can find the complete list of the changes at <http://www.ense…

ensembl biomart ensemblbiomart ensembl89 News

updated 8.3 years ago • Thomas Maurel

I sync my local R package library over Dropbox for easy switching between machines. Our group recently upgraded to Dropbox Business, which consequently changed the path to my library from ~/Dropbox/R/library to ~/"Dropbox...is BiocCheck version 1.11.7. BiocCheck is a work in progress. Output and severity of issues may change. Installing package... sh: -c: line 0: syntax error near unexpected to…

bioccheck bug

updated 8.3 years ago • Michael Steinbaugh

Biology Solutions using R and Bioconductor", R. Gentleman, et al., page 233 for some time and have recently run into some resistance from a colleague who claims that this type of filtering distorts FDR calculations because...is that, since this method tends to filter out genes with higher p values and/or lower fold changes, that it is sort of a sneaky way of accomplishing just that. Of course, fi…

updated 18.4 years ago • Mark W Kimpel

be merged. For example, peak chr1:100-300 will be merged with peak chr1:299-500. Is it possible to change this behavior, for example, requiring at least 50% bp overlap between the two peaks, so the above example won't merge? If

DiffBind ChIPseq

updated 4.3 years ago • zhenfeng.liu1

by the rma() command. This one could be fixed by my professor. It seemed that there have been some changes in the affy package. The fixed command (see file sam_analysis.r further down) is working on the old university computers...when and why these parameters are not longer supported by sam(). I could not find a very detailed change log of the siggenes package except of this one (http://fgc.lsi.u…

Prostate hgu133a2 probe affy siggenes ASSIGN Prostate hgu133a2 probe affy siggenes

updated 15.7 years ago • Torbjörn Klatt

I am converting murine gene lists to human genes using the code below from https://www.r-bloggers.com/2016/10/converting-mouse-to-human-gene-names-with-biomart-package/ ```r convertMouseGeneList <- function(x){ require("biomaRt") human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") genesV2 = getLDS(attributes…

biomaRt RNASeqData R

updated 3.4 years ago • Dina

<div class="preformatted">O/S: Windows XP R: 2.3.1 Bioconductor: 1.8 I'm trying to get a list of all probes in a given GO category. In the Bioconductor annotation libraries there are mapping from GO category to probe ID and from probe ID to GO category. I'm finding that they do not match in terms of annotation. Here's a sample script: library(hgu95av2) library(GO) # Get list of pro…

Annotation GO probe Category Annotation GO probe Category

updated 19.1 years ago • Daniel Gatti

with the lfc argument in the treat function I get different results. I do not know what the log fold change corresponds in my case? Any help is appreciated Thanks

limma multiple factor design

updated 10.2 years ago • ea1402

a p-value<0.05 at an FDR of 0.1 (the default)...Great!...but the problem is that when I try to change the FDR cut-off to something else I still get the same 2440 genes no matter what I set (i.e. alpha=0.5, alpha=0.01, ect.). I attempt...to change the FDR alpha value in the code as follows: res <- results(dds, contrast=c("Group","Group 1","Group 2"), alpha=0.01) &nbs…

deseq2

updated 10.0 years ago • polinski.mark

requires the following missing aesthetics: x, y if I provide those labels the points still don’t change <pre> t <- v + geom_point(aes(x=log10 y=log2 size =2))</pre> Using method two with csScatter works great and the points change size

cummerbund ggplot2 size r volcanoplot

updated 10.8 years ago • ianmisner17

The following code produces a case where the MAP estimate of the log fold-change is opposite in sign to the MLE estimate.  I know the fold-change is small in absolute terms, but it's still a little bit...The following code produces a case where the MAP estimate of the log fold-change is opposite in sign to the MLE estimate.  I know the fold-change is small in absolute terms, but…

deseq2 differential gene expression

updated 9.1 years ago • Gavin Kelly

I have a couple questions for a project I'm working on. First, I originally used the DESeq2 tool on a local instance of Galaxy (I find the GUI really easy to use, plus I can upload batches of featureCounts files rather than combining them manually). Today, I went to check my results by running it in R. Both were fresh installs, so they should be the newest version on their respective platforms (…

DESeq2

updated 2.4 years ago • murphytho1401

I notice in the paper (http://genomebiology.com/2010/11/2/R14) of Young et al. (2010) that, for the category GO:0016020 "Membrane", it ranks 1st using GOseq for total read counts adjustment (Table 4), while it ranks 702nd using...for different "bias.data" arguments? In the vignette of the goseq package, page 22, the top-6 categories using read counts adjustment match 3 categories of the top-6 ca…

GO Category goseq GO Category goseq

updated 14.2 years ago • Gu Mi

package for GO enrichment analysis (taking length bias into consideration). Those top-ranked categories are obtained based on the ranking of "over_represented_pvalues" from the goseq object. The goseq also includes...are determined? Why don't we consider "under-representation"? I am not sure if I can think of a category being "enriched" this way: if there are more DE genes for a particular categ…

GO Category goseq GO Category goseq

updated 14.2 years ago • Gu Mi

cost: 1 gamma: 0.002739726</pre> \` I am wondering if it possible somewhat to change SVM-kernal parameter in the \`geNetClassifier \` ? Thanks in advance

genet genetclassifier

updated 7.7 years ago • Seymoo

Hey, it's a boneheaded question, so please have mercy. How does limma calculate log2 fold change from the matrix of microarray probeset intensities? I am having trouble replicating fold changes of significant...The control samples are 1:8 The treatment samples are 9:12 How do I calculate log2 fold change given this example? Said another way, what series of equations are used to calculate t…

limma

updated 6.6 years ago • mat149

It seems that Affy is silently changing their procedure for the probeset annotation of HTA 2.0. <pre> <code>cut -d"," -f 1,10,13 HTA-2_0.<strong>na33</strong>.hg19.probeset.csv...Exonic normalization control (Positive Control)" </pre> The probesets in the "main" category are not affected by this changing, as their probeset\_name are the same as probeset\…

oligo pdInfoBuilder pd.hta.2.0

updated 10.1 years ago • tangboyun

I want to add a column with name "category" to my data, how can i do that? input: col1 col2 col3 col4 col5 1 20 + 4 6 2 24 - 6 7 .... output: col1 col2 col3 col4 col5 col6 1 20 + 4 6 category...2 24 - 6 7 category

name R column

updated 2.5 years ago • sat

Dear all, For whom is familiar with Agilent gene expression data, I would like to ask help. We recently received some Agilent gene expression data from our collaborators. For individual sample, there are 7 corresponding...columns: Unknown:Log(Ratio) Unknown:Ratio Unknown:Fold Change Unknown:Log(Error) Unknown:P-Value Unknown:Intensity 1 Unknown:Intensity 2 It seems that Ratio= Intensity1…

updated 17.2 years ago • affy snp

Hi, I recently got the new version of ChAMP 2.8.9 and now I can not proceed through champ.DMP, an error now occures that did not show...array of at least two dimensions</pre> I have the same data, nothing in my samples/sample sheet was changed. Any idea what might be the problem? Could it be the new version? Thanks in advance for any answers!! Sarka

champ

updated 8.1 years ago • sarka.vorackova

Hi everybody, I recently changed from DESeq to DESeq2 to perform my RNA-Seq analysis. I would like to know how I could include the baseMean values

deseq2

updated 5.6 years ago • leonardo.paganini

of 45 samples which represent 26 different conditions. I read that the calculation of the fold change in changed DESeq2 and affects the genes having low counts more than the highly expressed genes. However, I found genes...had zero counts in series of 4 samples (2 replicates in each of 2 conditions), while their log2fold change was 3. what is the reason for that? or how can this be prevented? I…

DESeq2 DESeq2

updated 11.7 years ago • Noa Henig

This is more a comment in case anyone else runs into this issue - I'm using Gviz to plot output from RepeatMasker, and the column of TE names...This is more a comment in case anyone else runs into this issue - I'm using Gviz to plot output from RepeatMasker, and the column of TE names is...make a note of it - is there something obvious that I am missing that would allow me to plot without changin…

gviz gff

updated 8.4 years ago • kbrevik

The behavior of BiocManager::install() for updates seems to have changed from biocLite(). Specifically, when biocLite() was executed under 'sudo R', any system R packages installed in /usr/lib/R...The behavior of BiocManager::install() for updates seems to have changed from biocLite(). Specifically, when biocLite() was executed under 'sudo R', any system R packages installed in /usr/lib/R were

BiocManager

updated 5.9 years ago • howarth.mailing.lists

preformatted">Dear all, The new Ensembl marts for release 75 are live on www.ensembl.org. You can change your host to access our most recent data: mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", path...Renamed Saccharomyces cerevisiae assembly from EF4 to R64-1-1 A complete list of the changes in release 75 can be found at http://www.ensembl.org/info/website/ne…

Saccharomyces cerevisiae Vega Saccharomyces cerevisiae Vega

updated 11.5 years ago • Thomas Maurel

div class="preformatted">Hi, I am using quite a lot the GEOquery libray. Recently I found out that the link to the GSE repository changed on GEO therefore the getGEOfile function fails to download...the file.Since there is not the possibility to change the download path in the getGEOfile it will be nice if the mantainers of GEOquery could add a parameter to the function

GEOquery GEOquery

updated 19.0 years ago • rcaloger

I am using DESeq2 to find the DE genes in a data set with 21 replicates ( 21 + 21, paired-design). I get the DE genes but with very small log2 fold changes (less than +/- 0.5) , as you can see in the plot below: <pre> > summary(resdds, 0.05) out of 22025 with nonzero total read count adjusted...set with 21 replicates ( 21 + 21, paired-design). I get the DE genes but with very sma…

deseq2 logfoldchange

updated 9.5 years ago • g.atla

time-course-experiments) and came up with a doubt regarding the criteria used to calculate the fold-changes and padj.  In this example the fission data package was used, which contains RNA-seq data for a time-course of fission...minute) resTC <- results(ddsTC) My question is: When you look to the calculated fold-changes, are they the average of the fold-changes for all the …

deseq2 timecourse

updated 7.9 years ago • santos.migueldm

log2foldChange\_knockdown\_Control\`. Is this logFC the logFC for the exon expression (i.e. includes changes in gene expression), or the exon usage?   Ian     &nbsp

dexseq

updated 7.9 years ago • i.sudbery

<div class="preformatted">In the package affycoretools, how does the function limma2annaffy determine which fold change to output in the case of multiple contrasts? In topTable, one can specify the coefficient, but I don't see that this is the...preformatted">In the package affycoretools, how does the function limma2annaffy determine which fold change to output in the case of multiple co…

affycoretools affycoretools

updated 19.4 years ago • Kimpel, Mark W

an annotation package for Affy 133plus2 reporting the number of synonymous & non synonymous changes for the genes on the array. If it does not exist does anybody has a good suggestion about how to retrive this information

Annotation affy Annotation affy

updated 18.4 years ago • marco zucchelli

there is no Gui available for the Unix version. It would be nice if somebody could tell me how to change the working directory on command line. Tapan Mehta</div

updated 22.3 years ago • Tapan Mehta

with differentially accessible peaks. I want to generate a data frame with all these peaks and fold changes to plot a fold change x fold change plot for 2 of the contrasts. dat <- dba.contrast(dat, group1=dat$masks$CON.treated...dat, bDB=TRUE) In the `dbSites$binding` I get the consensus peaks of both contrasts with the fold change. (also in `dbSites$peaks`) CHR START …

diffbind atac

updated 5.3 years ago • lindsaynhayes

Dear Community, i recently implemented treat & topTreat functions in a part of my specific microarray analysis, in order to use simultaneously...a fold change cutoff with a corrected p-value. Here's a small part of the code used: ... <pre> <code><span style="line-height:1.6">design1 <- model.matrix...design1, weights=aw) fit2 <- treat(fit,<strong>…

limma treat topTreat microarray

updated 9.3 years ago • svlachavas

I recently updated R and some packages and ran into a problem when trying to run GEOquery to download a dataset. When grabbing...featureData featureNames: 2315633 2315674 ... 7385696 (21787 total) fvarLabels: ID GB_LIST ... category (12 total) fvarMetadata: Column Description labelDescription experimentData: use 'experimentData(object)' Annotation

geoquery ncbi geo biobase

updated 6.8 years ago • cschot3

for samples (IPs) and input controls (SMI). We also have location information for all windows. Recently, we got feedback and ended up in two approaches and would appreciate your feedback what you think is the right thing...to do, or if you have any ideas or comments: **Approach 1)** In short, we estimate size factors, perform DESeq2 dispersion estimation and wald test. We modified DESe…

deseq2 ihw

updated 6.0 years ago • schwarzl

I have some code using snpsById from SNPlocs which worked under R 3.4.4/Bioconductor 3.6 which has now broken since upgrading to R-3.5.0/Bioconductor 3.7. I've not been able to find any documented change which may be responsible for this. The following snippet illustrates the problem: library("SNPlocs.Hsapiens.dbSNP144.GRCh37") snps<-c("rs429358"); snplocs<-SNPl…

software error snplocs gpos

updated 7.3 years ago • j.abbott

node attributes. However, when I tried to customize the edge attributes, it did really work. I can't change any of these attributes, including arrowhead, style (e.g. line style, dashed, solid etc), labelfontsize. I did see the edge...labels but their size was too big and I couldn't change it. I doubt other attributes would all work well. I noticed that other people reported something similar on M…

geneplotter Rgraphviz geneplotter Rgraphviz

updated 17.9 years ago • Luo Weijun

sample dots look a bit far away from each other although the 2 groups are still separable. How can I change the axis scales so I bring the samples in each group closer together? Thank you

deseq2

updated 5.6 years ago • nfaizo

quick-start In the guide, it says to use contrast (or name) because contrast sets the log fold change to 0. I have two conditions treatment and control. And for my dds$condition, I releveled it so that the ref = "control". I looked...apeglm and ashr to shrink my results, but my plots seem shifted up and the threshold (>2 fold change) looks curved (why??) Here is my unshrunken plot I …

DESeq2 MAplot

updated 2.6 years ago • La

fit) tt<-topTable(fit,adjust="fdr",n=6000) write.table(tt,file="tmp.txt",sep="\t") I have also recently read about the Kooperberg method for background correction. Is this a preferred method? I have been able to do this...fdr",n=32) tt<-topTable(fit,adjust="fdr",n=6000) write.table(tt,file="tmp.txt",sep="\t") I recently had a small argument with an advisor who told me to do backg…

limma Category limma Category

updated 20.3 years ago • lepalmer@notes.cc.sunysb.edu

Dear BioC experts, I'm trying to do an efficient counting of all possible nucleotide changes between aligned nucleotides from short-read sequencing and corresponding reference nucleotides, i.e. how many...rseq2) == maxqwidth qseq2 <- qseq2[masklen] rseq2 <- rseq2[masklen] ## tally nucleotide changes nt2 <- combn(DNA_BASES, 2) ntPairs <- apply(nt2, 2, paste, col…

GenomicAlignments Biostrings

updated 6.7 years ago • Robert Castelo

p>   <div style="direction: ltr;">when I try to run Gene set enrichment analysis for GO categories and KEGG pathway,</div> <div style="direction: ltr;"><span style="line-height:1.6"> I got the probes that I considered

GO KEGG

updated 9.8 years ago • libya.tahani

Hi, Is there a way to compare significant changes between sample without replicate ? Regards, Attis

fourcseq

updated 10.1 years ago • julienpontis

makes sense base on the fold. But also genes have peaks in both conditions which based on the fold change is not correct. Would you please have some comments? Thank you so much

DiffBind

updated 2.3 years ago • Chris

controls after summarization, when I reorder by concentration, and roughly calculate the log-fold change they are all close to 1?? My supposition is that I am overfitting the data with RMA and that I need to find a better normalization...and summarization methods that I should look at? Like iter-PLIER or FARMS or ? Any advice or comments are welcome. Thanks, Matt matthew.thornton at med.usc.ed…

Normalization xps Normalization xps

updated 11.2 years ago • Matthew Thornton

graphical output towards my needs. I therefore have 2 questions, and would appreciate if you could comment on these: 1. How do I change the scale at the image. I used this command: pv.out <- pathview(gene.data = as.matrix(dd2\[,7:22

pathways

updated 8.5 years ago • svmichaela

div class="preformatted">Edmund, On Thu, 24 Jun 2004, Edmund Chang wrote: > I am going through the tutorial now and I encountered a problem with > the top table > 'Error in unlist(multiget...know how to > correct this problem. Sorry, affylmGUI was using the "multiget" function which is recently been replaced by "mget". It is fixed in version 1.1.3, available from…

affylmGUI affylmGUI

updated 21.2 years ago • James Wettenhall