Bioconductor Forum

<div class="preformatted"><adv> Hi, March 2009 marks the 20th anniversary of the invention of the Web. Like all great inventions, it arises out of an unmet need that badly needed a solution. Tim Berners-Lee foresaw the great potential that can be unlocked by connecting data across disparate operating systems. You can see the full talk by Tim Berners-Lee as he explains it at: http://w…

updated 16.8 years ago • Anderson Brown

by SD) as is commonly done prior to clustering. During gene selection steps I typically use a fold-change cut off on a list of differentially expressed genes to further enrich the list for candidate genes with larger fold...changes. I have noticed a very strong positive correlation between fold-change and variance (i.e. genes with a big fold change...have big variances). However, when I plot the…

Clustering Clustering

updated 17.3 years ago • Johan van Heerden

are the a and b plots. It's like the "circular" isn't working, and I am not able to generate the categorie legend and the color of the edge either. I am able to put colors on the nodes with foldchange though, What I am missing...0.05, readable = TRUE ) color.params <- list(foldChange = foldChange) # Specify fold-change for coloring p <- cnetplot( go_enrichment, showCategory …

cnetplot DESeq2

updated 11 months ago • Blandine

predictors easier to compare to each other. My understanding is that this doesn't and shouldn't change anything about the model fit except the scale of the coefficient. When I do this in DESeq2, I find that it changes not only

deseq2 glm rescale

updated 5.6 years ago • jc.szamosi

ward.D2" , clustering_method_columns="ward.D2", row_dend_side = "left", top_annotation = ha) draw(a, merge_legend = TRUE) # join the two legends thank you

r rnaseq complexHeatmap annotation

updated 5.6 years ago • camillab.

expressed in control but which have high expression in treatment theoretically have an infinite fold-change. Preprossesing algorithms will provide numbers for fold-change for these genes, but to do this there seems to be an assumption...that the chip can reliably detect this. If this is not the case, then it would seem that the fold-change number the preprocessing algorithms provide for genes tha…

GO Preprocessing GO Preprocessing

updated 16.6 years ago • Matthew McCormack

div class="preformatted">This only affects people using the Source packages, not the Win32 packages. I made a minor change yesterday to the build scripts and realized I missed a minor change

GO GO

updated 23.4 years ago • Jeff Gentry

that allows me to use use HyperGTest with custom lists. All I have to turn the list of categories in to a binary matrix, where my rows are my genes, and the columns are the different categories and the entries in...gt; then what the man page says might apply to you and you might want to > start looking at the source code for the Category package to see what is > involved in defining…

Annotation Pathways GO Yeast convert GOstats Category Annotation Pathways GO Yeast

updated 16.9 years ago • Iain Wallace

3.2.2.  ggbio: I get the following error message when I try to install ggbio: <pre> > source("https://bioconductor.org/biocLite.R") Bioconductor version 3.0 (BiocInstaller 1.16.5), ?biocLite for help BiocInstaller...version 3.0 is too old for R version 3.2.2; remove.packages("BiocInstaller") then source("http://bioconductor.org/biocLite.R") A new version of Biocondu…

ggbio rnbeads rversion3.2.2

updated 10.1 years ago • areyoujokingme

keep getting alot of the following error messages: Note: No specified download type, defaulting to Source is this normal?? Kind regards Sam -- ---------- Samuel Lattimore Ph.D Postdoctoral Fellow Cancer Research UK Molecular Oncology

updated 22.2 years ago • Sam Lattimore

I recently updated my package Logolas in Bioc 3.7 (R 3,5) version. While that version works fine, a few of my R users complained...that the Bioc 3.6 ( R 3.4) version is now broken. I want to change the Bioc 3.6 version as well or at the least direct users to Bioc 3.7 somehow. What route should I take?   Thanks

Logolas old-version BiocUpgrade

updated 7.7 years ago • Kushal K Dey

I'm also struggling to find doc on what database it uses by default? I figured since 147 is the most recent it would be the best one to use. Am I using `` snpAnno `` incorrectly? Any help would be greatly appreciated! Thanks

minfi methylationepic illuminahumanmethylationepicanno.ilmn10b.hg19 SNP

updated 8.5 years ago • Ellen O

early 2007 with all your help Installed 64bit Intel MacOS stuff Installed the new BioC maanova stuff Changed one of the 60 chips And reran the mixed linear regression previously done in early 2007 The command was ftest.Breed.mix_1000perm081109...significant? I have 64bit R.app but to install the 64bit packages I quit R.app and in terminal do source ("http://www.bioconductor.org/biocLite.R") bio…

Regression probe gcrma PROcess maanova Regression probe gcrma PROcess maanova

updated 17.2 years ago • Loren Engrav

make it work. When using the package's readGAF function to create the list of gene sets from the GO categories with the Rat files downloaded from the GO webpage (http://www.geneontology.org/GO.downloads.annotations.shtml...expressed genes and these gene sets doesn't work, as it looks for matches between the 'symbol' category in the gene sets and the genes of interest. However, the numbers in the…

GO rat2302 Category mgsa GO rat2302 Category mgsa

updated 13.0 years ago • Guest User

div class="preformatted">There does not seem to be an option for changing the text used for cluster labels, so is there a workaround? I can change the dimnames of the centers (see below), but they

updated 12.0 years ago • lep

div class="preformatted">Hello, Is there a way to specify/change the significance level, i.e alpha, in ks.test so one can adjust for different alphas for different sample size? -- Shripad

updated 17.7 years ago • Shripad Sinari

Hello, I'm new to RMA. Can anyone tell me which command to use for finding out the fold changes for a given set of genes. thanks sachin.</div

updated 22.2 years ago • Sachin Mathur

Is it possible to change the email address linked to my account on the bioconductor support website? I don't see an option to change it when

bioconductor

updated 5.2 years ago • Leonard Goldstein

Hi for all, I am trying to fit NB2 model for taxa from an open-source, phyloseq object. I analyzed the taxa carefully, plotting histograms with log10 scale or clr. I tried to check the GOF...I think I am familiar with DESeq2 tutorial also but still, I am not an expert. Any suggestions or comments are highly appreciated

deseq2

updated 5.3 years ago • wisam.tariqsaleem

I would like to calculate shrunken log fold changes from RNA-seq data, and I recently ran in to the same case that was described in this old post by Mike Love: https://support.bioconductor.org...large fold changes. This scenario could occur in non-biological samples, for example technical replicates plus DE spike ins. The reason...would cause a problem is that the prior is formed according to a h…

RNASeq DESeq2

updated 3.6 years ago • Victor

Hi All, I am interested in calculating the logfold change from the transformed expression file obtained by using variance stabilizing transformation function.  I used...the data using a different statistical test than the one in Deseq, thus I cannot use the logfold change given by the differential analysis of Deseq.  Is there a straightforward conversion between the logfold c…

deseq2 logfoldchange variancestabilizingtransformation

updated 8.2 years ago • lirongrossmann

Hello, I have a question about influence of log2 fold change in determining best genes in differential expression of DEseq2,as an example with adjusted p-value < 0.1,I have...0.89% low counts \[2\] : 11375, 42% (mean count < 1) what is the best range of log2 fold change for selecting genes

deseq2

updated 8.9 years ago • elhamdallalbashi

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070312/ 9653e3be/attachment.pl

updated 18.8 years ago • Lana Schaffer

I recently started using minfi for analyzing a large set of 450k methylation arrays. For a small trial run, everything worked...missing, but with the bean plots, certain samples display the sample name, but the graph is blank. Changing the group labels changes which samples show up, so it's not a problem with the samples or the input object. Has anyone

minfi illumina illimina 450k methylation methylation

updated 9.8 years ago • igor

div class="preformatted">Hello, I am rerunning code I had using biomaRt. But I believe there is a change in the attributes. Before, everything was 'structure_xyz' from the Structure category: anno <- getBM(c("structure_gene_stable_id

biomaRt biomaRt

updated 17.4 years ago • Elizabeth Purdom

bioconductor/ limma developers I was wondering if there is a straightforward way of getting fold changes per gene set out when I run CAMERA or any of the gene set functions in limma. This is because I need to plot them. I am enjoying...using the general pipeline, but at the moment to get the fold changes I am having to code it out manually. Currently I am getting the log(TPMs) for every gene in…

limma

updated 8.0 years ago • chris86

class="preformatted">Hello, I am using the tracks function from ggbio package, but I am unable to change the size in the x axis. The df dataframe: chr start end id chr12 72065147 72204484 ENSBTAG00000045751 chr12 72529373...ylab = "Soft") + theme(text = element_text(size=20)) tracks(ex) In this example just the y axis in changed by theme (size =20). The x axis continues v…

ggbio

updated 11.3 years ago • Vinicius Henrique da Silva

Hello. Today, I am trying to perform a GSEA on a gene list deriving a human. The code and the result are here. ``` > HuSplCD103nEqCD103pEq_GSEA <- gseGO(geneList = HuSplCD103nEqCD103pEqRanking, + OrgDb = "org.Hs.eg.db", ont = "BP", keyType = "SYMBOL", pAdjustMethod="none") using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019)…

clusterProfiler

updated 19 months ago • sawa

is fine, but when I run with data from GSE68744, all the genes result with a positive fold change, while the command `summary(decideTests(fit))` says that I have ~800 up and ~1500 down DEG. Here's my code ``` > x <- read.maimages...files = targets, source = 'agilent', green.only=TRUE, path = 'data/GSE68744/GSE68744_RAW/', other.columns="gIsWellAboveBG") > y <- ba…

limma microarray foldchange DEG GEO

updated 5.9 years ago • Pietro

We recently ran into a problem of GOstats package: Below is how we performed GO enrichment analysis, both the background and...We recently ran into a problem of GOstats package: Below is how we performed GO enrichment analysis, both the background and input...function"’ Then we converted the input entrez\_ID to go\_id to manually sort out the genes in each category. We found th…

gostats

updated 11.2 years ago • ylc35

for Enriched GO term. I want to increase the font size for Cnet plot. I tried par(cex=0.1) nothing changed. I tried many different values. My output file is png. Thanks

clusterProfiler font size Tutorial

updated 6.7 years ago • bony.dekumar

div class="preformatted">hi i get an error when trying to install R 2.9.1 from source on an intel mac os 10.5.7. i have used the gcc4.2 from xcode 3.1 and gfortran 4.2 from http://r.research.att.com/tools...4.3 installed with macports. same error. im not an expert in this and im a bit lost as to the "source" of my problem? here follows some of the output from configure and make: ok-ulla:R-…

updated 16.4 years ago • Jesper Ryge

"Holger Schwender" writes: > Hi Seth, > > while following your suggestion and taking a look on the check > reports of siggenes 1.11.0 (for BioC 2.1) I found the following > note: > > checking R code for possible problems ... NOTE > filterALL: no visible binding for global variable 'ALL' > filterALL: no visible binding for global variable 'ALL' > . > . > . >…

Cancer annotate genefilter siggenes Cancer annotate genefilter siggenes

updated 18.7 years ago • Seth Falcon

the doc][1]. I now have tables of occurrence of domains for the various ```protein_domain_source``` categories: ```c("pfscan", "scanprosite", "superfamily", "pfam", "smart", "prints")```. Can someone comment on the availability of further annotation...of these sources, and where specifically they are taken from? I am using the ```PFAM.db``` package from which I can get ```Description``` …

ensembldb pfam.db

updated 5.7 years ago • bruce.moran

to you for having created such a useful piece of software. What I wanted to ask you is this: I recently came across [Adi Tarca's publication](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079217...sensitivity).  I was wondering whether these results are outdated, however, because in recent interactions on BioC support ([http://support.bioconductor.…

limma genesetenrichment

updated 9.8 years ago • Aditya

function within the Biobase package. File: $RHOME/library/Biobase/R/all.rda (On my intel MAC) Commenting out the message lines stops the startup message. 1) Backup original all.rda 2) Clear all packages from the search...onAttach function 5) save(list=ls(all.names=T), 'all.rda') I'm sure there are better ways of changing one function within a data file, but this one worked for me. Hope this …

updated 19.4 years ago • Alastair Droop

ctss9 0.128643307100390 + 1 chr1 14028 14029 ctss10 0.128643307100390 + 1* Recently I did an update of all the installed bioconductor packages using the commands source("http://bioconductor.org/biocLite.R...4608, chr1 40911858 40912963 ul49 0 + 0 0 0,0,0 1 1105, 0,* Is this a change made in the update, or the new version of *rtracklayer*c…

rtracklayer rtracklayer

updated 13.6 years ago • swaraj basu

Hi, once loaded a dba object, and already computed the counts, is there a way to change only the design conditions column in order to perform the further steps? I just want to shuffle the sample conditions

diffbind conditions edit

updated 6.5 years ago • inzirio

Identifier >Reporter Name Reporter Biosequence Type Reporter >actual Sequence Reporter Comment Reporter Group Role >Reporter Control Type CompositeSequence Identifier >CompositeSequence Name Composite...Sequence Comment] > >when i did: >dat <- read.maimages('filename',source >='genepix.custom') > >I get…

limma ArrayExpress limma ArrayExpress

updated 19.8 years ago • Gordon Smyth

package(s) 'GOstats' also installing the dependencies ???GSEABase???, ???genefilter???, ???XML???, ???Category???, ???annotate??? trying URL 'http://bioconductor.org/packages/2.13/bioc/src/contrib/GSE ABase_1.24.0.tar.gz' Content...Mb) opened URL ================================================== downloaded 2.7 Mb * installing *source* package ???XML??? ... ** package ???XML??? successfully unp…

GOstats GOstats

updated 12.2 years ago • Guest User

differential expression analysis. I already follow DESeq2 tutorial but I only get the fold change difference for 2 groups, normal and disease. So, the question is, I want to check the fold change to 1 of the sample as the...base. I imagine like this. I have 14 sample. I will have fold change for difference between 1 and 2, 1 and 3, and so on, until 1 and 14. So, is this method possible t…

deseq2

updated 10.7 years ago • bharata1803

gt; enough about R to do that. > > Jeff > > > On Jan 29, 2004, at 1:15 PM, Jeffrey Chang wrote: > >> Hello everybody, >> >> I'm trying to install Bioconductor into a freshly compiled R 1.8.1 on >> OS...X 10.3.2. I'm sourcing the getBioC.R from >> http://www.bioconductor.org and trying …

Cancer Biobase tkWidgets affy Cancer Biobase tkWidgets affy

updated 22.0 years ago • Wolfgang Huber

I am a new learner of DESEQ2 and have seen similar posts on this forum but could not find clear answers. What would be the best way to create heatmaps specifically with 2 log fold change(base 2) in DESEQ2 or R in general? In DESEQ2, heatmaps are created based on VST (Variance Stabilizing Transformation) values. The count data I've used is unnormalized raw counts from FeatureCounts. I would…

DESeq2

updated 2.5 years ago • bio2249

on older data because the original resource was removed from the the public domain before the most recent update was produced. This package should now be considered deprecated and future versions of Bioconductor may not...the following information: Plea to support KEGG http://www.kegg.jp/kegg/docs/plea.html and the comment in the Editorial of the NAR DB issue (Nucl. Acids Res. 2012 40 D1: D1-…

updated 14.0 years ago • Asta Laiho

We were asked [recently][1] what is the best practice for posting Salmon quantification files to GEO to allow for computational reproducibility...the sample `tar` file as the sample quantification file to GEO. Feel free to post questions/comments here. [1]: https://twitter.com/EloweDevo/status/1249728169290207234 [2]: https://twitter.com/EloweDevo/status/1250575311110103040

salmon tximeta Tutorial

updated 5.7 years ago • Michael Love

Thank you for your answer, that is very helpful. Is there any document/site that indicates these changes? I have seen changelogs before but wasn't able to find anything for SPIA. The reason that I ask is that I have just re-run...the bioconductor mailing list also. > I will give you the answer now anyhow. > > The main change from SPIA 1.4.0 to 1.6.0 is the KEGG pathway data…

Pathways SPIA Pathways SPIA

updated 15.3 years ago • Lavinia Gordon

on our site for free, or we can set up a private work area for you. It is also available as open source and runs on LAMP+R servers and OS X. Please contact me directly with questions etc, John email: john at mcneilco.com office

updated 19.1 years ago • John McNeil

differential expression of miRNAs between two different cell types when the composition of miRNAs changes drastically? How about if I am interested in how a particular treatment affects the expression of the most highly...or just across replicates? If I have many different treatments or cell types that drastically change the expression of highly expressed/dominant miRNAs does that change the vari…

limma voom

updated 9.9 years ago • Jake

div class="preformatted"> Hi, How to change the point size in the DataTrack? I changed the "cex" parameter in "DataTrack" but it seems no effect.My code is: dtrack &lt

updated 12.1 years ago • shao chunxuan

Hello,   Can I change the axis limits within the dba.plotVolcano function? Simply adding ylim=c(min,max) doesn't work. I made volcano plots...for two contrasts, and it would be nicer to have comparable axes. Is there any way to change it?   Thanks for your help, Suz   &nbsp

diffbind

updated 7.6 years ago • Suz

they are a better solution than the Git-SVN bridge: *  The mirrors contain complete commit history. *  The mirrors contain release branches for Bioconductor 3.0 and 3.1, and new releases will be added as they...mirrors (brought to you by the hard work of Jim Hester) and we hope you are too. Questions and comments are welcome on the [bioc-devel mailing list](h…

git github git-svn bridge subversion News

updated 10.6 years ago • Dan Tenenbaum

Hello, I have a multi-factor design and I have successfully used DESeq2 to extract my comparisons of interest.  I wanted to use DESeq1 in order to compare (long story) but I do not know how to extract specific comparisons.  THere is actually the following comment on the vignette: "Fixme: Can we add a paragraph on what to do if we only want to make speci c comparisons, e.g. let…

DESeq2 deseq

updated 10.6 years ago • ramiro.barrantes

div class="preformatted">Dear List, I have been trying to find GO category enrichment in one of my gene lists. The list is derived from hgu133a. When I run the function "GOHyperG", I get an error...lib = "hgu133a", what = "BP") 3: eval.with.vis(expr, envir, enclos) 2: eval.with.vis(ei, envir) 1: source("gostats.R", echo = T) ></div

GO hgu133a Category GO hgu133a Category

updated 20.8 years ago • Ramsi Haddad

8,000 features, RGU34A, RGU34B and RGU34C respectively. I want to combine this data with some more recent data from RAT2302 arrays. I understand I can combine the identifiers using some spreadsheets downloaded from the...The reason I want to combine the 3 RGU arrays is because I wish to (amongst other things) perform category analysis to make a comparison between the old data and the new data. A…

rat2302 rgu34a rgu34b rgu34c affy limma Category rat2302 rgu34a rgu34b rgu34c affy

updated 17.2 years ago • james perkins

reviews and detailed protein information. New pathways are added frequently. Check out our recent updatings of the BMP and FGF pathways on our pathways page. All our pathways are available in powerpoint format. Click...here to view a slideshow of some of our pathways. Our pathways are also searchable by category. See previews of our pathways: Akt Pathway Apoptosis in Drosophilia Transcripti…

Transcription Pathways Category Transcription Pathways Category

updated 13.7 years ago • Gita Singh

Unassigned_Nonjunction    0 Unassigned_Duplicate    0 </pre> This category means “_The fragment mapped to a region that is not annotated in the annotation file_”. To confirm it, I selected

rsubread

updated 9.8 years ago • Likai Mao

PcTxNlaUmAI). He had 2 suggestions: - Combine the two batch variables into one, if 3-4 reps are left in each batch - Use ComBat multiple times, adjusting for the first batch using the other batch variables as covariates...I cannot go with the first suggestion because combining the batch variables would create too many categories and I would not have enough replicates per batch category. I am s…

GO Category sva GO Category sva

updated 11.8 years ago • Guest User

div class="preformatted">I have recently explored the use of alternative CDFs from affyprobeminer (APM) or a 36 array dataset derived using the Affy rat2302...This list should, then, consist largely of random genes. To test this hypothesis, I used the Category package to test for over-representation of GO and KEGG categories in my various lists. What I found was a huge degree

GO rat2302 cdf affy qvalue GO rat2302 cdf affy qvalue

updated 17.7 years ago • Mark W Kimpel

Dear list, Using example from heatmap_2 (Heatplus) i could conduct a heatmap. However when i changed the color key according to a certain range, the labels on the color key didnt change. Is there a way to fix this? Thanks...mm, Rowv = NA, Colv = NA, scale="none", legend=1,col=heat.col[length(heat.col):1]) ## Change the color key to 0-7 ## would like color key on the legend t…

updated 16.8 years ago • Yen Ngo

happened: I run my DESEQ2 analysis with the full dataset and got genes with a certain log2fold change and pvalue via results(dds0). I then run the analysis again after removing some genes. We expected that the log2fold...change and pvalue would not change and that only the padj value would change. But all values changed.. Can anyone explain why

DESeq2

updated 4.1 years ago • Bine