Bioconductor Forum

Hi there, I am trying to analyse a data set to identify differentially expressed genes between plant development stages. Currently, I have generated the data for the...have less than 10 reads, rowSums calculates the sum of rows of a matrix or an array, counts is the number of occurences) dds <- ddsHTSeq[keep,] # This removed ~10 000 elements, reducing size of matrix dds$Stage <…

plant Transcriptomics DESeq2 r

updated 3.7 years ago • cicely.day

<div class="preformatted"> Dear Gurus, I am doing an Illumina microarray analysis. The study design is a 2x2 (i.e. varying on two different conditions). As part of the analysis I'm doing a GO analysis. There are a few GO categories of special interest, so I want to extract data for the probes identified in these categories and cluster the data. The problem is that after performing the GO …

Microarray GO Category Microarray GO Category

updated 12.8 years ago • Guest User

div class="preformatted">Hi Mustapha, I made the same erroneous conclusion in regards to software version numbers. As I was told, they are NOT decimal places, so since 10 > 9, R version 2.10 IS > 2.9. Which part of the version number...is increased for a new version depends on the amount of change from the previous version. There has to be some sort of major change to increase …

updated 15.9 years ago • Jenny Drnevich

Please Help!   Why does getGEO return "Error: Duplicate identifiers for rows"? How can this error be fixed?  This getGEO command was working fine for a week and then Stop working...R\\\\desktopBrstC") Found 1 file(s) GSE76275\_series\_matrix.txt.gz Using locally cached version: D:\\I\_\\\_Gene\\R\\desktopBrstC/GSE76275\_series\_matrix.txt.gz Error: Duplica…

getGEO

updated 8.0 years ago • cg

for org.Hs.egENSEMBL: org.Hs.egENSEMBL is an R object that contains mappings between Entrez Gene identifiers and Ensembl gene accession numbers. Help description for org.Hs.egENSEMBL2EG (it is the same help message): org.Hs.egENSEMBL...is an R object that contains mappings between Entrez Gene identifiers and Ensembl gene accession numbers. Help description for org.Hs.egSYMBOL: org.Hs.egSYMBOL i…

Annotation Annotation

updated 13.0 years ago • John St. John

a command or a package that can help me to retrieve the aminoacid sequence starting from the protein identifier, through a link with Uniprot or similar: Let's say I have : P10451 , Human I would like to obtain: MRIAVICFCL LGITCAIPVK...self.aspx/le%20PV%20in% 20viaggio!/89.JPG [[alternative HTML version deleted]] </div

updated 16.4 years ago • Giulio Di Giovanni

and SingleR packages to analyze my scRNAseq data. Everything works well and I was able to identify cell types in my samples with the following pred <- SingleR(test=merged, ref=ref, labels=ref$label.main) I am looking...for a way to look deeper and identify T cell subsets. any advices or suggested tutorials? thank you

cellsubset SingleR SingleCellExperiment

updated 4.9 years ago • achaillon

Hi, I am trying to use the Bioconductor package in R 3.6.3 on Windows 64-bit platform to analyse my RNA-seq data with Apis mellifera. I am facing difficulty from an error described below. I have checked the available GTF file, using readGFF, the gene_id comes in the 10th column. But that is how I have downloaded the file from: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/003/254/395/GCF…

featureCounts

updated 5.7 years ago • chatterjee.arumoy

5 males and 5 females for 4 tissue types (skin, liver, brain, and gonads), and I would like to: 1. Identify genes/transcripts with skin-biased expression 2. Identify genes/transcripts with sex-biased expression 3. Identify...look better) I then fit the model using glmQLFit: ``` fit <- glmQLFit(y, design) ``` To identify skin-specific genes, I then do: ``` skinVbrains <-…

edger

updated 6.4 years ago • spflanagan.phd

and how this number diminishes as the overlap criterion becomes more stringent (larger values of minOverlap), by calling dba.overlap...with mode=DBA_OLAP_RATE. This returns a vector containing the number of peaks that would be in a consensus peakset if minOverlap were set to the index (so the first element of the vector...the total number of merged peaks, as if minOverlap=1, the second element as…

DiffBind DiffBind

updated 11.8 years ago • Rory Stark

Bioconductor. Now, I want to add a column in the final output, which includes the gene accession number of reference sequence, for example, NM_008725 besides gene entrez ID and gene name. In this way, I could match probe ID...to their corresponding accession number. But how can I write a code to implement it? Thanks in advance. YiSong PS. library("annotate"); library("mouse4302.db"); tota…

probe limma probe limma

updated 15.3 years ago • Yisong Zhen

genes and comparing the resulting list to the gene universe will enable the testing procedure to identify regulated ontological processes, but it won't be able to identify whether the processes are upregulated or downregulated

PROcess GOstats PROcess GOstats

updated 11.8 years ago • Joseph Shaw

div class="preformatted">Hi, Is it normal not to have the same number of sequences in the fastq file and the object generated from readfastq? grep @ SRR062641.filt.fastq | wc -l 187786 &nbsp...nbsp;        S4 Thanks, Carol [[alternative HTML version deleted]] </div

updated 12.7 years ago • carol white

Hi all, I am trying to use PEER in R (on conda) to identify hidden confounders in the raw counts of my RNA-seq experiment. I am following their tutorial ( https://github.com/PMBio...I have installed R-PEER on Conda, but am having issues with following with the PEER pipeline, to identify 10 hidden confounders in my expression data. I was wondering if anyone could advise? I couldn't find much he…

PEER RNA-seq differential expression hidden confounders

updated 6.9 years ago • rodrigo.duarte88

with different subsets of the same data: subscript out of bounds arguments imply differing number of rows: 4, 6, 2 argument of length 0 arguments imply differing number of rows: 0, 8 As with these arguments it works depending...keepCol)[i]) }, error = function(e){message(e)}) </code></pre> I am using the latest R 3.4.2 version and the latest Bioconductor ver…

stategra

updated 8.0 years ago • Lluís Revilla Sancho

analysis was done using Deseq2 v1.2.10 and R v.3.0.2. Although we are still using the same version for Deseq2, R on our system is now upgraded to 3.2.1. Repeating exactly same analysis using the same code but with newer...version of R, gives me half the number of genes as significantly expressed.  Does anyone know why this discrepancy could

deseq2

updated 10.1 years ago • genomica

preformatted">Hi, The maPalette() function (in the marray package) does not always return the number of colors requested. More specifically, if a middle color is given and the number of colors requested is odd, then maPalette...returns either one more or one less than the requested number of colors: # >>> returns 12 colors <<< maPalette(low="white", …

marray marray

updated 15.5 years ago • Ali Tofigh

3/2/2013 8:20 AM, Anirban [guest] wrote: > Dear all, > > Is there any way to get all entrez identifiers that are annotated with KEGG pathways? Actually I am using GOStats package in R to perform KEGG pathway enrichment...In general, for each KEGG pathway term there is a list of annotated hgnc symbols or entrez identifiers.. For all KEGG pathway terms we must have one list of …

GOstats GOstats

updated 12.8 years ago • James W. MacDonald

4756990164 9130 6715201209 JJJ 1434 4756996655 1602 6715208737 Where the 1st column is the identifier, the 2nd column = observations 1, the 3rd column = background counts 1, the 4th column = observations 2 and the 5th column...c(as.integer(data[i, 2:5])), nrow = 2) : NAs introduced by coercion When I replace the large number in the 3rd and 5th column with smaller numbers, the…

updated 12.4 years ago • Gibbons, John G

<div class="preformatted">It looks like Biostrings function "writeFASTA" overwrites the output file at each run. It seems it does not support the "append" parameter. I have to generate one big file gathering a miRNA identifier and relative sequence followd by a variable number of dara records pertaining such a miRNA target genes transcription. Each record is made up of a 3'utr identifie…

Transcription miRNA Biostrings Transcription miRNA Biostrings

updated 16.4 years ago • mauede@alice.it

file that has not been preprocessed fully. However, perhaps because of minor changes, the resulting number of probes excluded changes from what I had documented in the past (using the same script). It seems my path forward should...be to use an older version of lumi (where can I find this) and try and see if that gives me the same number as before. How can I install this older version...Thanks, …

lumi lumi

updated 12.5 years ago • Juliet Hannah

I'm developing a new gene expression and survival analysis platform based on Bioconductor, but also including the custom annotation products from the BrainArray lab - http://brainarray.mbni.med.umich.edu - which could potentially become the new standard for some widely used microarray platforms. More use would also be made of the Gene Ontology, moving away from an emphasis on individual&…

installation

updated 11.1 years ago • robin073

in the range of 13-17 million reads. I was wondering if DESeq can handle this kind of difference in number of reads between samples? Or a down sampling of reads is necessary before DESeq? Regards, Rushiraj [[alternative HTML...version deleted]] </div

DESeq DESeq

updated 12.1 years ago • Rushiraj Manchiganti

<div class="preformatted">Hi All, Is there a way to identify the genes that contribute to the gene set enrichments calculated by roast/romer? I realize that all of the genes in...div class="preformatted">Hi All, Is there a way to identify the genes that contribute to the gene set enrichments calculated by roast/romer? I realize that all of the genes...a gene set, or something else alto…

updated 11.8 years ago • Stephen Hoang

Hello, I have a question about identifying highly variable genes after applying vst from deseq2. I don't think it makes much sense to find those genes after...variance stabilization. Should I identify the genes using counts or normalized counts and directly use the gene list on the post-vst data for any downstream

DESeq2

updated 2.4 years ago • MaXXinE

<div class="preformatted">Hi everyone, I am working with mRNA data from Affy 'drosophila2' arrays and miRNA data from Affy 'mirna3' arrays. I have identified a list of differentially expressed mRNAs and miRNAs. I'm having a bit of trouble with some downstream analyses and I'm hoping someone might be able to offer some help. I would like to use my list of differentially expressed miRNAs to…

miRNA affy microRNA miRNA affy microRNA

updated 12.7 years ago • Fiona

cancer in TCGAbiolinks. 1 file is downloaded. In the file I get with TCGAbiolinks, samples are identified with designations such as 75a8bcb9-cac9-4fee-8757-bb802f4d355f", and copy numbers are identified by -1,0,1. When I...use the TCGA web interface samples are identified by their sample numbers, and copy numbers are denoted by their actual inferred copy number 1,2, 10 etc. However they...xlsx)…

TCGAbiolinks cnv

updated 4.1 years ago • raf4

<div class="preformatted">Hello All, I am using DESeq for identify differentially expressed genes among a couple of samples. At the end of the calculations i write the results to 3...div class="preformatted">Hello All, I am using DESeq for identify differentially expressed genes among a couple of samples. At the end of the calculations i write the results to...last two lines of code …

DESeq DESeq

updated 13.7 years ago • OD

<div class="preformatted">Hi, I am new to bioconductor. Is there a good package/work flow that does copy number/LOH analysis for Affy 100K chips, starting from CEL files? I have 100K data from ~ 30 tumor samples; and I plan to download 100K trios data (90 healthy individuals) as normal references from Affymetrix website. Do I really need normal references for copy number/LOH analysis? Cheng…

affy affy

updated 15.0 years ago • array chip

am using reactome.db for over-representive enrichment test, so I wonder how I can get the total gene number for a given species in reactome.db. For example, how many human genes (unique Entrez Ids) are annotated in reactome.db...Is there any simple way to get this number besides counting the shared genes between the annotated genes from "reactomeEXTID2PATHID" and records from "org.Hs.egUNIGENE2EG…

Pathways Pathways

updated 13.3 years ago • Gilbert Feng

gt; exprs.rawData <- exprs(rawData) However, extracting the data itself gives me a different number of rows: > length(pNames) [1] 243982 > dim(exprs.rawData) [1] 292681 6 Ive verified that this result occurs using the sample...http://www.affymetrix.com/Auth/support/downloads/demo_data/mirna_3_sam ple_data.zip Shouldnt the number of probes in the CEL file be the s…

probe PROcess probe PROcess

updated 12.8 years ago • Vicky Fan

Is there a R package to identify long stretches of gaps (Ns) in human genome (hg19

bsgenome.hsapiens.ucsc.hg19 hg19

updated 8.1 years ago • addyS

it on my computer? I am running R2.3 on Mac OSX. I downloaded the source file for the latest version of the moe430a (moe430a_1.12.0.tar.gz) and tried to install it from the R menu. When I do library(moe430a), and moe430a...moe430a() Quality control information for moe430a Date built: Created: Sun Mar 26 00:22:20 2006 Number of probes: 22690 Probe number missmatch: moe430aACCNUM; moe430aCHRLO…

hgu133a hgu133plus2 moe430a moe430b rae230b probe hgu133a hgu133plus2 moe430a moe430b

updated 19.6 years ago • MARIA STALTERI

RNA-seq data???, gene FBgn0004449 is on reverse strand and the plot result shows that exonic part number is aggregated from right to left (bigger coordinate to smaller). But in vignette of DEXSeq for version 1.6.0, the example...gene used for plot, FBgn0010909, is also on negative strand but the exonic part number 1 starts from leftmost. For me I think first consequence is better to help me corre…

DEXSeq DEXSeq

updated 12.5 years ago • Guest User

step 2 sudo apt-get install gdebi-core # step 3 export R_VERSION=4.3.3 # step 4 - notice version number is latest version always for first installation curl -O https://cdn.rstudio.com/r/ubuntu-2204/pkgs/r-${R_VERSION...bin/Rscript /usr/local/bin/Rscript # step 9 - create Rscript symlink (first installation only) R --version # step 10 - verify R symlink Rscript --version # step…

bioconductor Install

updated 19 months ago • BioinfGuru

I would like to limit the number of displayed genes (so **not** the categories, which is easily done with showCategory) in the enrichplot heatplot, but have...Function to get my enriched gene sets and then passing that to heatplot. I don't want to limit the number of genes before the gse analysis itself and I also don't want to change the number of the maxGeneSetSize, but would like...ENSEMBL') h…

heatplot enrichplot

updated 2.9 years ago • Melanie

Hi everybody, I'm using DESeq2 through phyloseq to identify bacterial OTUs that are significantly differently present between treatments. Yesterday I updated R and all...Hi everybody, I'm using DESeq2 through phyloseq to identify bacterial OTUs that are significantly differently present between treatments. Yesterday I updated R and all my...Hi everybody, I'm using DESeq2 through phyloseq to id…

deseq2 phyloseq

updated 9.5 years ago • am39

div class="preformatted">Hi every body, I'm just wondering about the current upgrading of R versions. Actually, I have the R version 2.9, but the new version (R 2.10) is already availaible. Theoritically, a new version is...usually higher in number than the previous one, but in R versions this is not the case ! Since 2.10 (newer version edition) is lower than 2.9 (older...version) ! So, is th…

updated 15.9 years ago • Mustapha A.

div class="preformatted">Hi all, I am comparing a number of cell types, and am wanting to find the signature genes of each cell type. I used the limma package to do this. The signature...or other BioConductor package to do this. Thank you in advance, Wendy [[alternative HTML version deleted]] </div

limma limma

updated 14.7 years ago • Wendy Qiao

preformatted"> Hi, I'm trying to create a custom annotation package for arabidopsis using RefSeq identifiers with AnnotationDbi's function makeDBPackage. Everything runs smoothly but the generated package is empty...id type present in the fileName gb/ug/eg/refseq/gbNRef outputDir="doc/arabidopsis.anno", version="1.0.0", chipName="arabidopsis" ) One strange thing here is that if I try t…

Annotation GO Annotation GO

updated 14.9 years ago • Asta Laiho

clusterProfiler to do gene enrichment for a non-model species. After I annotated my gene sets to K numbers, I noticed different genes might be annotated as the same K number. Should I get the unique K number set to do gene enrichment...or use all K number to do functional enrichment? Will this influence my result? And I also need to get the K number for my whole genome to make...it as the back…

clusterProfiler

updated 4.9 years ago • XM

control="no interest", statCalc="arith", hkgCalc="arith") Error in caseM[hkgs[1], ] : incorrect number of dimensions Apart from the vignette, I didn't think I would need to identify hkgs in each sample?? What is odd is that I...me where I'm wrong. Respectfully, Franklin -- output of sessionInfo(): > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) …

ReadqPCR NormqPCR ReadqPCR NormqPCR

updated 12.7 years ago • Guest User

regarding the use of interaction term versus grouping with different betaPrior arguments using version 1\_14\_1. I'm still using DESEq2\_1.14.1. I've been working on differential expression analysis of drought-tolerance...expressed genes (DEGs) between the two genotypes in the QTL region under drought and we want to identify them. Specifically, we want to identify DEGs under dr…

deseq2 interaction term multiple groups betaprior

updated 7.6 years ago • tarun2

Hi, I'm using EBSeq-HMM to find DE genes. The problem is among 17611 genes, 16139 genes are identified as DE which is very unusual. My cutoff to filter genes out before detecting DE genes was to discard all those genes...model, I have to run this model by its default settings. What do you think accounts for this large number of DEGs found? Has anyone worked with this package before? I read the…

ebseq-hmm

updated 8.8 years ago • fa.gholizadeh89

I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version...I am getting an error while mapping the gene names to the StringDB identifiers using the map function. The code was working fine before with the StringDB version 11 but giving an error for version 11.…

PPI STRINGdb

updated 4.3 years ago • Ashish Jain

were collected at 4 different time points, which algorithms would you recommend in order **to identify the trends ?** thanks a lot, -~ Bogdan

RNASeq trend

updated 4.3 years ago • Bogdan

However due to the design of the snp.matrix it cannot store these log2ratios and associated Copy number. Is there an available package/class out there that has been created. I have spent some time looking at the bioconductor...list and can't seem to find one? Could I in theory alter the smlSet class to stored my own version of snp.matrix instead? Many thanks in advance, Nathan [[altern…

SNP GGtools SNP GGtools

updated 17.4 years ago • Nathan Harmston

preformatted">Dear Bioconductor community,    I am looking for a package that does Copy number along with LOH analysis (B allele frequency) for intensity files from SNP 6.0 arrays. Please direct me to the right package...for this kind of analysis. Thank you very much in advance Raj [[alternative HTML version deleted]] </div

SNP SNP

updated 13.5 years ago • Rajan Saini

<div class="preformatted">Dear Dennis, To find transcripts specific to one tissue versus the others, you need to test that tissue vs the others, but I'm sure you already know that. If you have replicates of each tissue, you can do pairwise comparisons between the tissues, and choose transcripts which are consistently up in one vs all the others. If you don't have replicates, there's no al…

edgeR edgeR

updated 14.5 years ago • Gordon Smyth

<div class="preformatted"> I'm getting an error that says "incorrect number of dimensions" when I try to use parLapply on a function that works fine on a single non- multicore node. I see that bug fixes...div class="preformatted"> I'm getting an error that says "incorrect number of dimensions" when I try to use parLapply on a function that works fine on a single non- multicore node. I se…

updated 12.1 years ago • Guest User

I had already posted that repository to your tracker. So, please help me solve it and link the new version of PhosMap to issue number 953. Many thanks

error github package contribution

updated 7.0 years ago • ecnuzdd

<div class="preformatted">Hi, I currently have a list of HUGO gene ids which relate to genes in areas of gain over a whole chromosome, and would like to perform GO enrichment analysis on them. So I have 2 problems: 1. currently i have been defining my gene universe based on affymetrix arrays, however now I am working over the whole genome. gene_universe = getBM(c("entrezgene"), mart = ens…

Annotation GO Annotation GO

updated 17.2 years ago • Nathan Harmston

pre> Hi,</pre> I have issues with the getIndices() function from the flowWorkspace package. It identifies much more cells as "TRUE" for a gate than it should. Here's my code: <pre> wspath<-"~/Desktop/workspc.wsp" ws<-openWorkspace...lt;-nodelist[num_f5] summary(getIndices(G[[1]],f5))</pre> I have no clue why getIndices() doesn't identify the right cell…

flowworkspace getIndices

updated 8.8 years ago • helena_t

I am doing transcriptome analysis of a non-model plant species. Is anyone can help me to get TAIR identifiers corresponding to my sequences? I have to blastx more than 20000 sequences. My input data is a fasta file containing...Vol 112, Issue 8 > ******************************************** [[alternative HTML version deleted]] </div

updated 13.5 years ago • Hers

my microarray data using limma and 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...a plot to represent of differential expression results ( Figure Contrast(3)), it is possible to identify significant genes.  So, Why does it happen? Sorry&nbsp…

Treat method Number of DE genes

updated 8.2 years ago • Sanches

1.6">Hi,</span> Somatic signatures package uses RSS and unexplained variance to assess the best number of signatures. In Alexandrov et al paper (Cell Reports 3, 246-259) they used cosine similarity and Frobenius reconstruction...error to determine the number of signatures. Did any one compare the two ways and find difference in determination of number of signatures? Thank

somaticsignatures

updated 10.3 years ago • Asma rabe

I'm looking to retrieve metadata for all versions of each package, including their dependencies, from Bioconductor. Specifically, I need this data in a structured...JSON format that includes project names, version numbers, and corresponding dependencies. I am aware of the Bioconductor API but am unsure of the best way to use it to

metaMSdata

updated 16 months ago • Sadman

I've plotted pca plots with just using the plot() function as well, but I still do not know how to identify the particular sample that is the outlier. Any ideas for both affycoretools() or the general plot() function will be

updated 13.2 years ago • Guest User

Li, Hua wrote: > Hi, Francois, > Yes, if I know one protein in a specific pathway, how to identify > all the other members? > I appreciate your help!!! > Hua > > ________________________________ > > From: Francois...Li, Hua > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] how to find the children identif…

Microarray Annotation Pathways GO Microarray Annotation Pathways GO

updated 18.6 years ago • Francois Pepin

Hi all, From GEO study ID, I can find the microarray platform ID used. Then I can identify the microarray library to map probe ids in CEL files to gene symbols. For example, for GEO study GSE6731, http://www.ncbi.nlm.nih.gov...geo/query/acc.cgi?acc=GSE6731 The platform used is \`\[HG\_U95Av2\] Affymetrix Human Genome U95 Version 2 Array\`, <span style="line-height:1.6">then in &…

limma microarray annotation bioconductor annotate

updated 9.6 years ago • lijin.abc