Bioconductor Forum

extremely dynamic area etc., I'm somewhat worried whether this is actually possible. Does this much change in less than a year sound realistic to list members, or should I start bug hunting? Thank you! alexander Alexander.Ploner

Microarray Microarray

updated 22.9 years ago • Alexander Ploner

like to find all genes that show less than a 2fold increase in condition A vs B, wether the fold change is positive or negative. (and reciprocally genes that show not a 2fold decrease). Is that possible? I tried results

DESeq2

updated 11.0 years ago • samuel collombet

growth over 4 biological replicates per each condition. A collaborator constructed a graph of fold change from that output for approximately 15 genes of interest. I have a request from a peer reviewer to provide error bars

rnaseq deseq2 deseq standard error confidence interval

updated 9.9 years ago • lisa.crossman

count data, and I generate my dds object from phyloseq. _dds = phyloseq\_to\_deseq2(mouth, ~ category)_   I am interested in performing tests of how OTUs/species in different oral diseases within the mouth differ...5 different disease states including normal.    I have defined "normal" as the reference category as follows: _dds$category <- relevel(dds$categ…

deseq2

updated 8.9 years ago • negic4

bioc-devel at r-project.org >>> Subject: Re: [Bioc-devel] knowing what is changed/new in release patches >>> >>> A package may choose to provide a NEWS file which you should be able >>> to...gt; is optional how detailed it is, but this is intended to be a readable >>> summary of changes. &…

IRanges IRanges

updated 13.3 years ago • Malcolm Cook

dear All, was there any change to the biomart web service recently? Today I stumbled over the following problem when I wanted to list all available...line 4 and html 6: Premature end of data in tag html line 2 ></pre> I guess something had changed at the biomart web service.   cheers, jo   My R/Bioconductor: <pre> > sessionInfo() R versio…

biomart bug

updated 9.8 years ago • Johannes Rainer

abs(log2FoldChange) > lfc.cutoff_0.5) >up_padj_ ``` But I have exactly same results if I change the order and use "dpi14tocv" as baseline Can someone help me to understand why?? Thanks

deseq2 contrast DEG

updated 6.3 years ago • ire.ontiveros

we're currently using. On the other hand, our method works well in our hands! So you see my dilemma... changing something that works in order to make some savings... Any comments appreciated! Jose -- Dr. Jose I. de las Heras Email: J.delasHeras

Microarray Microarray

updated 18.6 years ago • J.delasHeras@ed.ac.uk

genes but instead they are reported to be significantly differentially expressed with huge fold changes. Has someone experienced this before or have any advice on how do account for such genes with large variation in counts

DESeq2

updated 24 months ago • Sneha

to produce pie charts or similar with percentage of genes associated to selected Gene Ontologies categories (or KEGG), preferable if I can choose the categories so that I can customise them using some search by keyword option...like to do it to compare the percentage of genes expressed in two different samples for the selected categories. I have explored Voronto (outside Bioc) and goProfiles and …

goProfiles GeneAnswers goProfiles GeneAnswers

updated 13.1 years ago • Jose M Garcia Manteiga

<div class="preformatted">Hi all, It looks as if the as.vector call to a run length encoded factor turns it to a vector of characters. Did this happen on accident, or was it a deliberate design decision? Previously: R-2.12, IRanges_1.7.19, GenomicRanges_1.1.20 (A factor of length one is returned): R> a <- Rle(strand(c('+', '-', '+', '+', '-'))) R> as.vector(a[1]) […

Cancer Cancer

updated 15.5 years ago • Steve Lianoglou

that GOstats hyperGTest comes out with. Am I right in thinking the p-value is for enrichment of each category individually (i.e. NOT corrected for multiple testing)? I'm analyzing array CGH data so I am testing a lot of categories...my universe is all human genes that have a chromosome position, GO category and entrez ID). Below is an example result - my interpretation is that I shouldn't get s…

Annotation GO Cancer CGH GOstats Annotation GO Cancer CGH GOstats

updated 18.2 years ago • Janet Young

div class="preformatted">Hi Jim,I fully understand your comments. I thought I made a Reply-all, but I will pay more attention next time. Sorry for the inconvenience. Maria > Date: Fri...gt; > Many thanks for your quick and very comprehensive response. > > > > From your comments, I have one more question related: > > > > (…

Transcription Annotation Normalization GO hgu133plus2 affy PROcess Category Transcription

updated 12.2 years ago • María Maqueda González

I found all the data are negative, the downstream function only works on positive value. How can I change the parameter of `vsn` , them the output can be positive value? Thank you in advance for great help! Best, Yue <img alt="Screenshot

vsn

updated 5.2 years ago • yueli7

scater package, that I am using for single-cell RNAseq analysis of 10X data.  I wish to change the size of the points and also remove the gray outlines that currently appear around the points. I tried using "scale

scater rnaseq single-cell

updated 7.9 years ago • CodeAway

deployLocation=*illuminahiseq_rnaseqv2*][name=*Level_3*]'</pre>   1. Is this because of the recent changes in TCGA? TCGA has posted the following info on their website " 06/10/2016 - __Announcement :- ____As the

tcgabiolinks tcgadownload

updated 9.6 years ago • sabarinath.chandrasekharan

all, I am a PhD candidate in Beijing Institute of Genomics, Chinese Academy of Sciences. Recently I have been worked with data analysis concerning RNA capture followed by high throughput sequencing. Four samples...for my project, I could just calculate RPKM value for each gene, and identify DEGs simply by fold change > 2? Thank you! Sincerely, …

Sequencing DESeq Sequencing DESeq

updated 12.5 years ago • 邵建明

at="gmail.com="> > To: bioconductor at r-project.org > Subject: \[BioC\] edgeR: fold change reported by exactTest for zero values of rna-seq > > I have used the exact test in edgeR to compute the log fold changes...expression in all samples > belonging to one of the two conditions. This would make the fold change > mathematically …

edgeR

updated 11.2 years ago • Gordon Smyth

black agouti3 129 black agouti5 129 black I want to test which genes change their expression when the environment changes, controlling for the genetic background. I am using DESeq2 for this...environment. However, the choice of the base level for the factors in my experimental design changes the genes that are significant. If I leave the default reference levels (129 for g…

RNASeq Genetics DESeq2 RNASeq Genetics DESeq2

updated 11.4 years ago • Guest User

3 replicates for each sample, choosing DESeq2 as the analysis method), peaks with very small Fold-change were found to be statistically significant. I have plotted an MA plot; the red points are the significant ones, the black...I'd like to ask whether you agree that it's surprising/strange that lots of peaks with a very small change became significant. There are no non-significant peaks above…

DESeq2 DiffBind

updated 5.1 years ago • Sam

Best wishes Gordon On Thu, April 27, 2006 2:00 am, Jenny Drnevich wrote: > Hi everyone, > > Comments from Naomi and Gordon (below) about the technical replication in > the 2x2 factorial loop experiment are very close...replicates, which leads to artificially lower p-values. This > combined with even minor changes to the variance components can lead to > …

Microarray limma Microarray limma

updated 19.8 years ago • Gordon Smyth

Hi there! I have a differential expression data set, consisting of a list of gene handles, their log2-fold expression change between two conditions, a p-value for that change, and annotated GO terms. It looks basically like this: https://www.dropbox.com/s/bswzujqx07t4lr2/VirtualBox_ubuntubox_11_11_2020_12_44_16.png?dl=0 I am currently working in R, and would like to do a GO term enrichm…

foldchange topGO DifferentialExpression enrichment

updated 5.3 years ago • lessismore

I look at the statues and see that most genes are category 4 ```r > table(normalisedData[["convergence"]]) 0 1 2 3 4 3049 516 4615 1 8098 ``` Category 4 is "baseline selection didn't coverge

Convergence DegNorm

updated 4.8 years ago • Dario Strbenac

Hello, Is there a way to test for differential binding above a log2 fold change threshold in the dba.analyze() portion of DiffBind? I understand we could use the fold argument in dba.report() to extract...in one group over the other. According to Section 2.12 ("Differential expression above a fold-change threshold") of the edgeR user's guide, such hypotheses should undergo thresholded t…

diffbind

updated 9.7 years ago • le2336

<div class="preformatted">Dear list, I am getting an error when trying to parse the latest msigdb version from Broad. I suspect the problem is due to that Broad added another category (c6). Will the new category be included in GSEABase? Is there a way to parse only categories c1-c5, or an alternative way to get all categories? See the R code and versions below. Thank you! Best regards, …

GO Infrastructure hgu95av2 Biobase annotate graph Category AnnotationDbi BiocGenerics GO

updated 13.1 years ago • Lina Hultin-Rosenberg

Hello Bioconductor community, I have used DESeq2 to test for differences in the overall transcriptional activity of species in a microbiome sample. However, i am not quite sure whether what I'm doing is correct. Thus, I would be very thankful for somebody confirming that this solution makes sense or pointing me to an error. I am comparing two different biological conditions. For each condition,…

Metagenomics DESeq2 Metatranscriptomics

updated 4.9 years ago • Tom

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; > pathways, but unfortunately none showing me how define my own very > > limited set of categories. > > You are exactly right, in that I want to …

Annotation Pathways GO Yeast convert GOstats Category Annotation Pathways GO Yeast

updated 17.0 years ago • Iain Wallace

the dosage and working mechanism of soma visit here at Health Naturo: [https://healthnaturo.com/category/soma-pills/][1] [1]: https://healthnaturo.com/category/soma-pills

TOP

updated 2.4 years ago • healthnaturo1

for the 5 odd columns of interest, and NULL for the 77 odd unwanted columns in a gpr file The change is to the following code in read.marrayRaw: comment out; # h <- strsplit(readLines(f, n = skip + 1), split = sep) # h <- as.list(unlist

updated 22.7 years ago • Marcus Davy

I have used the exact test in edgeR to compute the log fold changes. Here is the snippet: <pre> d <- DGEList(counts=counts, group=samples$Condition) d <- calcNormFactors(d) d <- estimateCommonDisp...in all samples belonging to one of the two conditions. This would make the fold change mathematically undefined (di…

edgeR

updated 11.2 years ago • Nick N

group B, hence contrast B versus A logFC =4 with adjusted-P = 10^-20). I am concerned that such fold-changes may be exaggerated. I am aware that voom calculates CPM using a prior.count of only 0.5, whereas the cpm() function uses

limma

updated 3.1 years ago • vm

<div class="preformatted">Dear Lukas and Bioconductors, I have been asked to look at a MeDIP-Seq dataset that has been processed with a previous version of the MEDIPS package (version 1.2.0) and I've noticed there have been some changes with regards to the current version I have installed (version 1.10.0). In particular, it appears as though the whole concept of AMS (absolute methylation …

Sequencing MEDIPS Sequencing MEDIPS

updated 12.5 years ago • Jonathan Ellis

seems* to work under 1.8.0, but you are welcome to report odd things you would notice). We made some recent changes in our code to try to speed it up (because it was slooooow, and still is), which hopefully did not introduce bugs

affy affy

updated 22.4 years ago • Laurent Gautier

gr <- GRanges(seqnames = c("1", "2"), IRanges(start=c(1000, 2000), width=100), strand = c("+", "+"), category = c("A", "B")) I would like to split `` gr `` based on `` category ``, in order to have a `` GRangesList `` that would be similar to: grl <- GRangesList

granges

updated 7.3 years ago • unamourdeswann

<div class="preformatted">Hello BioCer's, I've been using affycoretools, particularly limma2annaffy,for a while now and love it. These wrappers really make life simpler. However (there was bound to be a however), in a recent experiment I've had some problems with vennSelect. The experiment has 4 groups and 4 time points, 5 replicates each. There...love it. These wrappers really make l…

GO Survival annotate genefilter affy graph gcrma annaffy RBGL GOstats biomaRt affyio

updated 17.7 years ago • PeadarÓGaora

Hi, I have a list of differentially bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the condition and specific FDR cutoffs. If anyone has advice on how to...bound sites between conditions and would like to export lists defined by 2 things: fold change between some positive or negative value given the con…

diffbind

updated 9.1 years ago • rbronste

<div class="preformatted">Hi. Below is an outline of the code I am using to analyse two colour array data. Normal = Cy3 Case = Cy5 There are 3 replicates. Can the fold change be reported back in the siggenes.table? From the documentation, it is not obvious how this is done. Thank you for any help...to analyse two colour array data. Normal = Cy3 Case = Cy5 There are 3 replicates. Can the …

siggenes impute siggenes impute

updated 15.5 years ago • brian snail

have checked both the box and MA plots using both raw and normalized counts and there is very little change.  I am looking at H3K27me3 ChIP-seq data between two different tumor subtypes (i.e BRAF vs RAS). When using edgeR many...lt;- dba.count(dba, fragmentSize = 1000, minOverlap = 2) dba.contrast <- dba.contrast(dba.count, categories = DBA\_TISSUE) \#DESEQ2 dba.analyze &l…

diffbind

updated 9.3 years ago • cnova1950

odd when plotting tracks on a pdf device (postscript turns out fine), this only happens to some recent R-devel versions (tested on three r-devel builds Feb.3, Feb.14 and Feb.18), apparently the build machine in Seattle is...not yet affected, which has a devel build on Jan.15. This happens to the most recent devel version of Gviz 1.7.7. Here is an example, can't really figure it why, ############…

Gviz Gviz

updated 12.0 years ago • Dan Du

just greyed out. Data is a csv file with two columns: gene name in KEGG format, then log2fold change values in the second column. Code is below.![enter image description here][1] ```r > data <- read.csv("pathview_input_AN_OX.csv...header=FALSE) > geneList = data[,2] #importing fold change data as a vector > names(geneList) = as.character(data[,1]) #addin…

pathview Proteomics

updated 12 months ago • Jessica

I'm trying to run a straightforward Wald test in `` DESeq2 `` and was a little surprised to see that fold changes and standard errors are no longer shrunken by default. I know I can still compute moderated values using the `` lfcShrink() `` function, but I see no straightforward way to: a) calculate the corresponding test statistics and _p_-values; or b) implement the gene filtering, LFC thresh…

deseq2

updated 8.2 years ago • david.watson

enrichment for my data which is not built-in oraganism. >enriched.GO=unsorted_L14.15_S_GO.wall$category[p.adjust(unsorted_L14. 15_S_GO.wall$over_ represented_pvalue, method="BH") < 0.05] > head(enriched.GO) character...BP", "GO:MF"), method="Wallenius", repcnt=2000, use_genes_without_cat=TRUE) Using manually entered categories. Calculating the p-values... > head(unsor…

GO Category goseq GO Category goseq

updated 11.6 years ago • Guest User

Hi, I am trying to address the question which genes associate with change of the metabolite levels following the diet. I have paired samples (before and after the diet). I have previously asked...factors (at least a RIN) ``` design <- model.matrix( ~ ID + RIN + Timepoint) ``` 2) Gordon commented previously ``` "Even if you included Metabolite in a completely different non-paired …

edger

updated 5.4 years ago • anna.cot.anna.cot

arrange(desc(logFC)) ``` ```{r} library(msigdbr) hs_immune_df <- msigdbr(species = "Homo sapiens", category = "C7", subcategory = "IMMUNESIGDB") ``` ```{r} ranks <- deframe(res2) head(ranks, 20) ``` ```{r} fgsea_SHH <- fgsea(pathways = hs_immune_df, stats...r} library(clusterProfiler) ``` ```{r} hs_immune_df <- …

NanoStringDiff clusterProfiler fgsea

updated 2.8 years ago • pg45863

of bioconductor developers, if there is a function to generate a heatmap of all enriched GO categories after a conditional hyperGTest. For example, I have 5 different time points time-series data and with 3 different...doses. I run HyperGTest and I endup with atleast 50 categories for 5 time points and 3 drug treatments. 3hr @ d1; 3hr @ D2 ; 3 hr @ D3 - 50, 50 ,50 cats respectively. Like wise …

GO Visualization GOstats GO Visualization GOstats

updated 18.1 years ago • Srinivas Iyyer

TopologyGSA, DEGraph, clipper, SPIA, TAPPA, PRS, PWEA with a custom list of fold-changes and associated p-values rather than having these functions run a DE analysis internally? It doesn't seem so from the

ToPASeq

updated 9.1 years ago • rubi

for differential expression and found that DESeq2 mysteriously inverted the sign of a subset of fold changes. According to [this discussion][1], turning off fold change shrinkage should make log2foldchange from DESeq2 be simply...counts group B) / (mean of normalized counts group A). However, it seems that some degree of fold change moderation is done even when betaPrior is False. As an example…

DESeq2

updated 5.1 years ago • Yanling

when I try to re-run old scripts. I've never had this issue before, but updated from 2.6.1 to 2.7.0 recently. Any help/comments would be much appreciated! The full list of commands + sessionInfo is shown below. I've tried with

BUS BUS

updated 18.1 years ago • Helen Zhou

Phred+64,FastqQuality=Phred+33) is",score_sys,"\n") it is a Phred+64 system, how can i change the qual to Phred+33. then i can make new reads by reads <- ShortReadQ(sread=seqs, quality=qual, id= BStringSet(paste0(sample

updated 11.8 years ago • wang peter

Hi all, Can anyone point me into the direction on how to achieve the subject line? I'm using right now the "CustomEndNodeList" from "goTools", retrieve two consecutive ranks and accept only what I retrieve with the higher rank and not with the lower ... but GO has rank-skipping connections and I would prefer to really be able to slice the tree at level x below ID y while disregarding those ... …

GO GO

updated 17.7 years ago • Johannes Graumann

Hi Josh, I was wondering whether you got any response to this problem. It is quite old, but I just encountered the same problem. If so, I would appreciate it, if you can help Thanks, Assa [[alternative HTML version deleted]]

updated 15.0 years ago • Assa Yeroslaviz

Hi Josh, I was wondering whether you got any response to this problem. It is quite old, but I just encountered the same problem. If so, I would appreciate it, if you can help Thanks, Assa Assa Yeroslaviz Application service, Bioinformatics group Max Planck Institute for the Biology of Aging Robert-Koch-Str. 21 50931 Cologne Germany phone: +49 221 47889793 e-mail: AYeroslaviz at age.mpg.de

updated 15.0 years ago • AYeroslaviz

<div class="preformatted"> Hello Bioconductor Users, Sorry to bother you, but I have a couple of quick questions on the affy package that I have been unable to answer by reading through the textual description of affy available on the bioconductor website and the recent papers on the subject. Iin general, am very impressed with the noise reduction using affy and truly appreciate the Bioco…

Normalization probe affy Normalization probe affy

updated 22.9 years ago • Luckey, John

<div class="preformatted">Hello Bioconductor Users, Sorry to bother you, but I have a couple of quick questions on the affy package that I have been unable to answer by reading through the textual description of affy available on the bioconductor website and the recent papers on the subject. Iin general, am very impressed with the noise reduction using affy and truly appreciate the Biocond…

Normalization probe affy Normalization probe affy

updated 23.0 years ago • Luckey, John

<div class="preformatted">On Wed, Oct 02, 2002 at 02:09:00PM +0200, Jesper Ryge wrote: > Hi laurent > > I am using the affy package for R. I just have one question. I tried to > read a cell file and plot it with image(cel.file). That works fine, except > the image is turned upside down! It is a rat neuro chip, so there is a > control sequence i…

hu6800 affy hu6800 affy

updated 23.4 years ago • Laurent Gautier

appreciate your advice on the results(contrast) section of my analysis.  I have 5 disease categories(RM, RP, SP\_progress, SP\_stable and healthy) for each category we extracted monocytes and treated these monocytes...within each group by comparing monocytes with different treatment compositions (Eg: For disease category RM, I am interested in comparing 10nm vs 100nm, 10nm vs 50nm, 100n…

deseq2 deseq

updated 8.2 years ago • hrishi27n

Hi, I am running into truncated phenotype categories when I use GRASP2 like this: <pre> > library(grasp2db) > GRASP2() %>% tbl(., 'study') %>% filter(PaperPhenotypeDescription...in cystic fibrosis </pre> </td> </tr> <tr> <td> <p> </p> <p>Although cystic fibrosis-related categories in GRASP web page are…

grasp2 grasp2db annotationhub

updated 10.3 years ago • gokcen.eraslan

Hello, In a previous version, I was able to read a tabix file, including the first line that started with # and had column names. Now with Rsamtools 1.8.4, it skips that line and the first element of the character vector is the first record of the tabix file. Any way to get the old behaviour back so that I can know the column names ? anno <- "http://genomesavant.com/savant/data/hg18/hg18.ref…

updated 13.7 years ago • Dario Strbenac

How to extract top DEG using limma at threshold value p<0.05 and fold change >1.5 ? I request you all too kindly suggest the R script for topTable. topTable(fit2, coef=2, ……?????????) Thanking you. &nbsp

limma microarray R bioconductor

updated 8.7 years ago • rkp

nbsp; I have just read the vignette about DESeq2 and I have a question about shrunken log fold changes and threshold test. I use DESeq() and results() functions to get the gene set with absolute LFC > 1. I understood that the

deseq2 lfcshrink lfcthreshold differential gene expression

updated 7.3 years ago • corentinrichard374369