Bioconductor Forum

chloroplasts. That means that the mapping will be done on the chloroplastic genome (around 80 genes) and so the DE analysis. I was wondering if there is a minimum number of genes to be considered to have a correct DESeq2 analysis

DEseq2

updated 7.3 years ago • stefanie.graindorge

a 2-colour cDNA whole genome array for Anopheles gambiae (mosquito). The .gal file only has ensembl gene and transcript IDs for each spot; in addition since the chip was made, a number of the genes on it have been removed from ensembl...the annotation; in the meantime, however, I would like to know: How can I used the current ensembl gene list for An. gambiae to: (a) filter out (remove) those …

GO annotate limma GO annotate limma

updated 19.9 years ago • Amy Mikhail

div class="preformatted">Dear All, I'm very confused with the use of housekeeping gene. Can anyone give me some detail? Thank a lots Zhao</div

updated 22.0 years ago • zhao luo

function to obtain the graphical output for clustering. How do I then obtain lists of the genes that contributed to the different clusters? Thank you

masigpro clustering

updated 9.5 years ago • ls299

26136914 hsa-mir-503 24 133508024 133508094 I was hoping to use biomaRt to extract information for genes upstream and downstream of these miRNAs (see script below). I have created a list in the correct form for a multi filter...the miR id, start and stop #we have to extend the start and stop sites by 500000 #then retrieve genes in these regions starts<-as.numeric(mirRow[,3]) stops&l…

biomaRt biomaRt

updated 16.6 years ago • Iain Gallagher

group A, while a variety of pathway types are enriched in group B. When looking at the "leading edge" genes, it turns out that the genes responsible for the enrichment of energy-related pathways in group A are highly expressed...genes (in both groups), while the genes responsible for the enrichment of a variety of pathways in group B are expressed at substantially...about the following possibilit…

scRNA scRNAseq

updated 2.5 years ago • Omer

Hello, I would like to use edgeR for differential Gene expression analysis.  I have read counts data on 50 individuals in three biological replicates. I would like to filter...out lowly expressed genes. Is there a threshold to define express genes?   I was thinking to use CPM of >=2, and it should be in two of the three libraries...R code? Secondly, I would like to o…

edger rnaseq

updated 8.8 years ago • myprogramming2016

Why are these genes missing? HLA-A https://www.ncbi.nlm.nih.gov/gene/3105 HLA-B https://www.ncbi.nlm.nih.gov/gene/3106 For example, I found...with the same functions. ``` r library(TxDb.Hsapiens.UCSC.hg38.knownGene) regions <- genes(TxDb.Hsapiens.UCSC.hg38.knownGene) regions$gene_id[1:5] #> [1] "1" "10" "100" "1000" "100009613" ids…

HLA TxDb.Hsapiens.UCSC.hg38.knownGene

updated 6.0 years ago • Kamil Slowikowski

robust estimation of exon levels will require much greater sequencing depth; assuming that a gene has on average about ten exons, then you would need about ten times more reads to get a similar magnitude of counts. If you...don't have that data or are not interested in within-gene structural differences, gene level estimates may be the better choice. Of course, you could try out both and compare…

QuasR QuasR

updated 12.2 years ago • Michael Stadler

div class="preformatted">Hello, The attached file is the Probe Set IDs related to Human Gene 1.1 ST array. May someone let me know where I could find a .CSV file that includes both Probe Set IDs and gene names for this

probe probe

updated 12.2 years ago • Shahla Ghaumipour

I want to look at an RNA-seq data-set on `1 condition` to look for expressed genes. As there is only one condition, I can’t perform differential analysis. The only thing I can think to do is set a threshold...i.e. all replicates must have > 10 gene counts) then say these are expressed. But I don’t think this is a very good way of doing it. Do you know of any better ways that

RNASeq Gene ExpressionData

updated 4.2 years ago • AZ

<div class="preformatted">Hi All, I have two matrices   A and B. A contains expression values for 1000 genes in 10 conditions A[1:1000,1:10] B contains metabolic profiles of 100 metabolites in 10 conditions B[1:100,1:10] Is there a way...preformatted">Hi All, I have two matrices   A and B. A contains expression values for 1000 genes in 10 conditions A[1:1000,1:10] B …

updated 13.9 years ago • pankaj borah

Hi, I have run my initial analysis without filtering for low-expressing genes, given DESeq2's independent filtering procedure. Due to the low number of significant genes returned when using an FDR...Hi, I have run my initial analysis without filtering for low-expressing genes, given DESeq2's independent filtering procedure. Due to the low number of significant genes returned when using an FDR…

DESeq2 lowcountgenes deseq2 independent

updated 3.1 years ago • erbrocato

of all, I got some raw FeatureCount data, and there are multiple entries of the same meta-feature (gene) all with the same or very similar counts. What does this mean?  How do I combine them or remove them so that I only have...data for one meta-feature (gene)? Also, the raw data includes novel unannotated "genes". How do I remove these so that I can analyze only the annotated genes

rna-seq featurecounts

updated 11.0 years ago • ccheung

form the circle size, number of segments and segment width for a Circos plot when using a subset of genes, rather than hg19/18 as an anchor. Thanks

geneexpression genesetenrichment segAnglePo

updated 11.1 years ago • Peter.Wood

with biomaRt and I can't figure out what's going on. I am using getBM to pull down a large number of gene coordinates, and filtering to restrict to chromosomes 1-22 and X,Y. For some reason this procedure (which is giving no errors...is not pulling down some genes that I think it should. My basic code for pulling down all of this information is: tempAll<-getBM(c("ensembl_gene_id...biotype…

biomaRt biomaRt

updated 17.4 years ago • Elizabeth Purdom

using Repitools, but I am running into some issues with how to properly define promoter regions for genes with multiple isoforms with different transcription start sites. I'm working with the human hg38 Ensembl transcript...annotations. Suppose a particular gene has 3 isoforms, A, B, and C. Isoforms A and B have the same TSS and differ only in the splicing of exons farther downstream. Isoform...R…

repitools promoter tss annotation

updated 7.8 years ago • Ryan C. Thompson

div class="preformatted">Dear All, I'm looking to make a summary of the functionality of a gene (ID,name,position,Ch,function,pathways). could you please give me some useful informations (packages) to do this summary

updated 14.8 years ago • Mohamed Lajnef

Hi I am trying to follow through this post as an exercise to find genes that are not differentially expressed. Few things in this post does not work \[anymore\]. Can somehow help ? [1](https://github.com

deseq2

updated 7.1 years ago • evocanres

I have list of dysregulated genes in a disease. I want to find OMIM ID of disease associated with this gene. Some thing like as below. <table border="0" cellpadding...0" cellpadding="0" cellspacing="0" style="width:1779px"> <tbody> <tr> <td>Disorder name</td> <td>Gene symbols</td> <td>OMIM ID</td> <td>Cytogenetic location</td> <…

microarray omim gene disorder

updated 10.8 years ago • pankajnarula84

<div class="preformatted">Hi, I m currently trying to run some clustering on some expression arrays and I was wondering about the best way of doing it, I have 81 samples on hgu133plus2 (55000), I have filtered this down to approximately 10000 (X, Y, low variabilty, control probes), and wanted to try hierarchical clustering on these both by arrays and genes. I was planning on using hopach a…

Clustering hopach Clustering hopach

updated 17.5 years ago • Nathan Harmston

gt; cuff\_data CuffSet instance with:      0 samples      0 genes      0 isoforms      0 TSS      0 CDS      0 promoters      0 splicing...gt; cuff\_data CuffSet instance with: &am…

cummeRbund rna seq anaylsis r cufdiff

updated 8.5 years ago • bhagyathimmappa

package in R please. I have sequenced RNA transcripts from six separate species and am comparing gene expression between pairs of species. The issue I am facing is that I cannot work out how to account for gene length when...they were raw read counts. To do so, I calculated the reads per kilobase (RPK) using: read count / gene length Then the TPM using: (RPK / sum of all RPK of sample…

Normalization DESeq2

updated 2.3 years ago • cm15245

I have recently noticed a small discrepancy in the number of genes when running EnrichGO: the resulting GeneRatio column has 65 as the denominator (eg. 3/65, 12/65, 7/65...), however, in the dataframe...i fed into the enrichGO() function there was clearly 71 rows (genes) heres my code: enrichGO(gene = df$ENTREZID, OrgDb = org.Hs.eg.db, …

GO clusterProfiler

updated 17 months ago • Danté

div class="preformatted">Hi, In limma, one can use decideTests to assign each gene up/down/NC coded as 1/-1/0, and then use vennCounts to count the number of genes for each pattern. My question is, how can one actually...extract a list of genes with a particular pattern? For example, if I'm looking at 3 contrasts, and I want all the genes that are significantly up

limma ASSIGN limma ASSIGN

updated 19.9 years ago • He, Yiwen NIH/CIT

Hi list, Please forgive if this was asked before. In R, is there a way to find out how many Human gene products in a GO term (including all its children) like those reported in AmiGo? I'm talking about ALL the gene products, not

affy affy

updated 17.3 years ago • Shi, Tao

Dear community, I am using "minet" for gene module analysis. The following code gives the global network (returned by aracne(mim,eps=0.1)) as in the "net" object. In order...to detect gene modules, can I apply clustering methods on the global network, such as hierarchical clustering? mim <- build.mim(data

minet module

updated 6.1 years ago • zhang.jianhai

div class="preformatted">Hi, suppose I have a list of gene names like below, is there a "fuzzy"-matching based algorithm to convert gene name to locuslink id's? > head(anno[,4]) [1] Comp Rheb

convert convert

updated 18.6 years ago • Weiwei Shi

and batch effect corrected RNA-seq count dataset and I want to identify the Differentially expressed genes I have noticed that many workflows\packages to identifying Differentially expressed genes take RNA-seq count row

identifyingDifferentiallyexpressedgenes DESeq2

updated 4.9 years ago • MOHAMMAD

Hello, I have the list of gene IDs which are ensembl Ids I wanted do GO analysis for this list of genes. How can I do this from the GOseq I went through vignette...which is running the GOseq from the DE genes output, my genes list are not from the DE this are obtained according to my objective. can anyone suggest me? Gene IDs list...ENSMUSG00000074182 ENSMUSG00000078453 code What I hav…

goseq

updated 4.8 years ago • Lucky

Hello, is there an easy way to query an annotated Expression-Set by Gene-Symbols etc. to extract the Expression-Values for a single gene? I tried to annotate the row-names of the Expression-Matrix

expressionset bioconductor

updated 9.3 years ago • bi_Scholar

Dear Bioconductor users, I am writing to ask a small query to do with the retrieval of detectable genes in illumina data using "Lumi" package. I have a data of just over 43000 features and roughly about 26.5% of the genes are detectable...P value of 1% (according to the QC summary). My question is how to retrieve only the detectable genes and still have them as a lumiBatch object i.e. need to s…

Cancer Cancer

updated 18.5 years ago • Zara Ghazoui

of the situation. Suppose you do a limma analysis (say) with contrasts AvsB and CvsD. You select genes which are DE for AvsB controlling the FDR at 0.01, and similarly for CvsD. Now you want to look at genes the intersection...i.e., genes which are DE for both AvsB and CvsD. Unfortunately there is no way to compute the FDR for the genes in the intersection...2006 > >Hi, We have…

Bayesian limma Bayesian limma

updated 19.2 years ago • Gordon Smyth

div class="preformatted"> Hi all, I am just wondering how to process replicate genes in an array using limma package. each gene is printed twice on an array. For example, the actual number of genes is 19000...in my dataset, since there are replicate genes, I have 38400 spots (genes) in my dataset. I am just wondering how I can get 19000 genes from these 38400 genes before or after...normal…

limma PROcess limma PROcess

updated 21.9 years ago • p hu

preformatted">Hello, unfortunately I have I big problem I can't solve. I have to analyze if a gene is tissue specific. For example for the gene xyz I have following expression values: Heart Liver Brain ....several others...1/2 1 -1/2 C3 -1/2 -1/2 1 to get tissue specific genes, some p-values are exact 0 (even I…

BRAIN BRAIN

updated 17.5 years ago • Pascal Gellert

I would like to normalize everything (all 18,000 probesets) with RMA, but then only examine the 180 genes involved in ion transport. These are custom affy chips, and not sufficiently annotated for me to use GO, but I know which...genes I care about. I can readily generate the list with expression values using Ion <- exprs(eset)[c(234,17172,1006...), ], but don't know...limma. Is this doabl…

GO affy limma GO affy limma

updated 19.7 years ago • Heather Erika Hallen

column fields that describe the overlap. However if there is an overlap with a gene start, then I want to return the gene start and end locations as well as its chromosome and strand. Any help would be much...appreciated.  The code below should be pretty straightforward to understand. `` Genes `` is a GRanges object with gene attributes (e.g. start, end, strand, chromosome) and…

iranges R granges

updated 8.4 years ago • ssabri

<div class="preformatted">Hi, I was trying to get the genes annotated to the GO term "GO:0031281". My code: library(org.Hs.eg.db) genes <- get("GO:0031281", org.Hs.egGO2EG) When I run the code, I get: > genes <- get("GO:0031281", org.Hs.egGO2EG) Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :   value for "GO:0031281" not found If...div class="preform…

GO Homo sapiens GO Homo sapiens

updated 11.8 years ago • Tim Smith

div class="preformatted">Hello, I am using limma to select differentially expressed genes. I have 24 arrays and 40k genes. According to the limma users' guide, "If none of the raw p-value are less than 1/G, where G is the...number of genes, then all of the adjusted p-values will be equal to 1". I get raw p-values which are less than 1/G after applying eBayes; however...is 0.66. Does that me…

limma limma

updated 20.4 years ago • Lourdes Peña Castillo

in total. In the past I worked with time course and/or limma to detect differentially expressed genes. Are there any packages which you would recommend for the detection of differentially expressed genes? Would be nice

limma limma

updated 13.2 years ago • Peter Kupfer

div class="preformatted">Hi everyone, Does anyone know how to go from gene name to ENSEMBL ID? I'm using lumi to analyze my microarray data, however the names get changed from NuID to gene name when

Microarray GO lumi Microarray GO lumi

updated 12.2 years ago • Kripa R

I am new to R and am trying to use the Variant Annotation package to annotate my list of SNPs to genes within a distance of 50kb. For the intergenic SNPs, there are several gene values/IDs listed under the PRECEDEID and FOLLOWID...if anyone could suggest a solution to this? The intronic SNPs were successfully converted to gene symbols, only the intergenic ones with more than 1 gene were not succe…

annotation variantannotation rstudio

updated 9.9 years ago • noor.suaini

the package [**singscore**][1], in particular the function `simpleScore`, that allows to score a gene expression dataset based on one or two gene sets, I was wondering if the signature scores from different gene sets are...comparable. Say I have 4 gene sets that I use to classify tumor samples to molecular subtypes, my idea is to score the gene expression dataset with each...one of the 4 gene …

singscore GSVA GSEA subtypes geneset

updated 5.0 years ago • Pietro

such nice packages. I would like to know if limma fit function could be used with smaller set of genes or other metabolites quantified by liquid chromatography. I use limma in genes lists with thousand of genes, and never...in small sample sets. For instance, 2  or more groups; 4 biological replicates each, 150 genes/metabolites. Can we use empirical Bayes moderation in this situation? …

limma metabolite data moderated t-test

updated 8.5 years ago • iglezer

everyone, I am looking at one of the ImmGen RNASeq dataset and I am looking at a specific subset of genes, corresponding to a family of interest. The first step I performed was to subset the counts for the genes that I wanted...1357 genes) and then plot the PCA for the samples for that (I had to add a pseudocount in order for it to run). The results were the following...DE in the full dataset …

DESeq2 RNASeq

updated 2.9 years ago • andrebolerbarros

estimate the size factors only with the spike-ins and use it to normalize the counts of the other genes.  In my case, I am suspecting a global shift in gene expression, so is it correct to use internal controls (instead of

deseq2 differential gene expression controls references

updated 7.1 years ago • cris.kgs

of now, however, i dont know what is best analysis package of biocondcutor for detection of fusion gene mutation(eg. ALK) . if you know the best practice of analysis for detection of fusion gene in frame work of Bioconductor, would

bioconductor quasr

updated 9.5 years ago • maedakus

called `` eset ``, whose annotation is `` mta10stprobeset.db ``. When I try to map the probesets to Entrez IDs  as `` mta10stprobesetENTREZID(featureNames(eset)) ``, I get the error: <code>Error in .checkKeys(value, Lkeys(x), x@ifnotfound

mta10 entrez gene identifiers

updated 10.1 years ago • jacorvar

Since looking at the row variance and DESeq2 both act as ranking mechanisms for genes, is there any sense to taking the top 1000 or 5000 genes with the highest variance across samples from an RNA sequenced...set and running the DESeq2 pipeline on that subset to look for differential genes between groups (so simple design ~condition)? Thanks!&nbsp

deseq2 variance genes

updated 8.2 years ago • hs.lansdell

Hi all, meth() function in RnBeads package accepts an option 'type' which can be set to "sites", "genes", etc. When 'type' is set to "genes", how does it compute a single beta-value representing the methylation on single gene (e.g

rnbeads

updated 9.0 years ago • Tom

in a dataset. What I'm now wondering is if I can use the same methodology to find co-regulated genes / genes with common transcription factors? I'd assume its simply of redefining the gene set gsc <- GeneSetCollection...eset, setType = CoRegulatedGenesOrSomeFunctionLikeThat()) I suppose what I'm asking is if such a gene set exists in Bioconductor? And if not can this be done somewhere e…

Transcription Pathways Transcription Pathways

updated 17.0 years ago • Paul Geeleher

div class="preformatted">I have an expression matrix confined to the genes I wish to plot e.g. sample1 sample2 ... gene 1 gene 2 ... This may be a simple question, but is there a single command to do gene expression

Cancer Cancer

updated 18.8 years ago • Daniel Brewer

IPR019954" and feeding that into retrain(), I now have the 4th model (most complete?), built using genes: 5667 of 5667 features: 4007 level detectors: 78 This obsoletes my Questions 3 and 4 from my previous email. However, Questions...generated models I now have, which one is theoretically better to use? The one with the most genes, most level detectors, or most features (domains)? Or the one w…

Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway

updated 15.4 years ago • Bogdan

We continue to run experiments like the ones I asked about a few months ago ([here](https://support.bioconductor.org/p/62973/)). One of the latest comparisons is between two different compounds in the same cell line. We would like to find those genes that behave differently when comparing between the two. If I follow the suggested logic for figuring out the contrast to use, I get the following: …

deseq2 rnaseq statistics

updated 10.3 years ago • sunkid

voom/limma workflow to analyse my RNA-seq data. Now, I want to do further analysis, like measuring genes correlation and try some machine learning method (regression, random forest, etc.). My question is, is the output of voom...nbsp;vRnaSeq$E   From the code above, what I understand is the exprs variable is a matrix of genes x sample for the log of gene expression. Is this data good f…

limma voom rnaseq

updated 10.0 years ago • bharata1803

I'd like to ask a question. What is the best way to reduce the number of differentially expressed genes? As you can see below, I have used the ___treat______ method___ to reduce it and no differentially expressed genes...of differential expression results ( Figure Contrast(3)), it is possible to identify significant genes.  So, Why does it happen? Sorry for my …

Treat method Number of DE genes

updated 8.3 years ago • Sanches

When I run DESeq2 to call differential expression in my data set, I get this strange pattern. I have two experimental conditions, "NM" and "IVF". When I compare them, you can see in the TPM plot that differential expression in very highly expressed genes is almost completely in the NM group, whereas DE in lowly expressed genes is in the IVF group (highlighted in navy). This seems like it could be…

DESeq2

updated 3.2 years ago • b88dfe53

perform a filter from my microarray data?  If I use the UniProt ID to filter replicated genes, is it correct? Thanks in advances &nbsp

Filtering Genes

updated 8.3 years ago • Sanches

Hello. I am trying to remove the gene names from a heat map I generated because there are many genes, and the gene names on the right side of my heatmap do not correspond

DESeq2

updated 4.5 years ago • Emma

Usually, I use q-value<=0.05 and |FC|>2 as the criteria to screen differentially expressed genes. If I want to identify genes with similar expression under different conditions, which criteria should I use? I was thinking...of only using q-value>0.05. But there are also some genes with |FC|~1 and q-value<=0.05. Thank you very much

deseq2

updated 5.9 years ago • wangy660