Bioconductor Forum

get that DNAStringSet object back into a fasta format for downstream analysis, keeping the original identifiers, appended with a number/letter, to give a unique name to each disambiguated sequence. I have been playing with DECIPHER...string or SQLiteConnection. Once I get the conversion figured out, I will work on how to make the identifiers unique! Thanks for any suggestions

DECIPHER FASTA disambiguate

updated 5.5 years ago • joannew

results of running the following in an R session sessionInfo( ) ``` Toop Loan customer Care number=9732430098//8658221735//♋call Toop Loan customer Care number=9732430098//8658221735//♋call

Mu

updated 2.6 years ago • Vfohgf

validate splicing events. I am using SNPlocs.Hsapiens.dbSNP144.GRCh37 and injectSNSPs to identify regions with genomic variants (to avoid placing the primers on them). So far, so good. However, the number of SNPs is very

snp snplocs

updated 9.1 years ago • arubio

If I have two groups of small molecules with different properties, e.g. one can penetrate membranes and the other cannot, and I have an m × n matrix of m small molecules and n descriptors (e.g. polar surface area, molecular weight), can I use, say, limma to identify descriptors that differ between these two groups? So basically, I would just be using limma on molecular descriptors instead of gene…

limma edger deseq2 cheminformatics

updated 7.3 years ago • perdedorium

<div class="preformatted">Hi all, I was following the tutorial flowWorkFlow.pdf to analyze flow cytometry data and I have the following problem: when I launch: > qp1 <- qaProcess.marginevents(flowData, channels = c("FSC-A", + "SSC-A"), outdir = dest, pdf = TRUE, sum.dimensions = c(5, + 3)) R say: computing margin events... Error in strsplit(iInf, " ")[[1]] : subscript out …

updated 15.2 years ago • drambald

ll need to keep any eye on in downstream analysis. In the subtitle of each plot I've reported the number of droplets exclusively identified in `e0` (`|e0_only|`) or exclusively identified in `e1` (`|e1_only|`) as non-empty. ![MA plots for...stand out: - Barcode plots - The barcode rank plots all look okay, with the knee point well-identified even when there are small 'kinks' in the pl…

DropletUtils emptyDrops scRNA scRNAseq 10x

updated 3.3 years ago • Peter Hickey

I am trying to install DESeq2 but it is not available for current R version. Did anyone have this problem and have a good solution? The same is in case of WGCNA package. I tried other methods of...I am trying to install DESeq2 but it is not available for current R version. Did anyone have this problem and have a good solution? The same is in case of WGCNA package. I tried other methods of install…

DESeq2

updated 3.2 years ago • annamariabugaj

Hi, I am trying to install the DESeq package on the R version 3.2.4 And receive the response "there is no DESeq2 package for R version 3.2.4 As well as I do not succeed to install

deseq2

updated 9.0 years ago • Mark.bogen

<div class="preformatted">Dear all, This is possibly more of an R question,but because it involves dealing properly with Affy probeset identifiers i'm asking here... Can anyone explain the rules R uses to replace '_' characters with '.'s? I am finding that columns in data frames are sometimes having there rownames changed from '1007_s_at' to 'X1007.s.at' (for example, lines 3-6 in the exce…

Cancer affy Cancer affy

updated 22.3 years ago • Claire Wilson

up&down=1500 2. up=200, down=650 When I tried different datasets, there were cases where the number of up-regulated genes was higher than the number of down-regulated genes in the t-test, while the number of up and down...1. Generally, t-tests are less strict in terms of test power than parametric tests, so the number of DEGs in t-tests is expected to be higher than in DEseq2. So, why…

DESeq2 statistics rna-seq

updated 2.6 years ago • SH

s from for example Human microarray 19K human >ESTs >and find out the corresponding accession number and subsequently Unigene >identifier. >I would like to keep a database of this information. You can download the...www.affymetrix.com/analysis/download_center.affx". The file contains mappings to GenBank accession numbers, Unigene ids, and other information. > …

Microarray Annotation GUI annotate widgetTools AnnBuilder Microarray Annotation GUI

updated 22.0 years ago • John Zhang

genes. summary(dme_sam,1.7) SAM Analysis for the Two-Class Unpaired Case Assuming Unequal Variances Number of variables having a fold change >= 1.5 or <= 0.6667 : 26 s0 = 0.0514 (The 0 % quantile of the s values.) Number of permutations...20 (complete permutation) MEAN number of falsely called variables is computed. Delta: 1.7 cutlow: -6.087 cutup: 2.896 p0: 0 Identified G…

miRNA affy siggenes miRNA affy siggenes

updated 14.6 years ago • Assa Yeroslaviz

repository of windows binary files of previous Bioconductor Packages? I would like to get previous versions of some Bioconductor packages, eg Limma 2.9.8 and I do not know how to find them. Thanks in advance Pedro Carmona </div

limma limma

updated 18.6 years ago • Pedro Carmona

Pokketme Loan Customer Care Number 8260061863=8346839852. Call 24x7Pokketme Loan Customer Care Number 8260061863=8346839852. Call 24x7

lpNet

updated 2.6 years ago • Dinesh

m running RNA-Seq data analysis using the old tuxedo protocol, which requires cummeRbund. My current version is 2.18 (not working for me), but I want to install 2.12.1 (this version works for me). Any suggestions on how it can be done

rna-seq cummerbund

updated 8.3 years ago • vinayjrao

the following problem while installing the following (or other) old packages? I have using latest versions of Bioconductor and R. -- output of sessionInfo(): install.packages("hom.Sc.inp.db") Warning in install.packages : package...hom.Sc.inp.db' is not available (for R version 3.0.2) -- Sent via the guest posting facility at bioconductor.org. </div

updated 11.8 years ago • Guest User

annotatedPeak_reorder, IDs2Add, by.x = "feature", : 'by.x' and 'by.y' specify different numbers of columns _______________________________ Nhu Quynh T. Tran, Ph.D. Assistant Professor of Preventive Medicine...1361 Fax: 901-448-7041 Email: qtran1@uthsc.edu<mailto:qtran1@uthsc.edu> [[alternative HTML version deleted]] </mailto:qtran1@uthsc.edu></div

ChIPSeq biomaRt chipseq ChIPSeq biomaRt chipseq

updated 11.4 years ago • Tran, Nhu Quynh T

Hi,   I have used two different versions of DESeq2 (1.16 and 1.18) and they give me completely different results loosing a lot of differentially expressed

deseq2 mikelove

updated 7.8 years ago • marika.catapano

hello, I need to install an old bioconductor version 2.6 version (_https://support.bioconductor.org/ _) I have installed R-2.12 in my windows. I tried to install one package

R

updated 9.8 years ago • Yuan Jian

div class="preformatted">Hi, I copied the older version I had for "hgu133atagprobe" and it worked with the current version of R and Bioconductor! Perhaps someone may want to

updated 20.1 years ago • Lana Schaffer

Hi, I would like to install edgeR version 3.16.5. I am using following code to install, but getting a warning message.  Could you please help me? source("https...biocLite("edgeRv3.16.5")  __Warning message: package ‘edgeRv3.16.5’ is not available (for R version 3.3.3) __   Thanks YP

edger

updated 8.5 years ago • myprogramming2016

has the same content as file "mature.fa" that can be downloaded from MirBase for Homo Sapiens miRNA identifiers and sequences. Whereas dataset "hsTargets" contains all target genes for Homo Sapiens miRNAs listed in file...mauede@alice.it wrote: > I'd like to figure out the difference between validated miRNAs whose identifiers only differ by a "*". See the following from miRbase (http:/…

miRNA Homo sapiens biomaRt microRNA miRNA Homo sapiens biomaRt microRNA

updated 16.1 years ago • mauede@alice.it

<div class="preformatted">Folks, I've been asked to install bioconductor packages with an existing installation of R-1.9.1. The downloaded getBioC() function refuses to work with this older version of R. Where can I find an older getBioC() which will allow me to install the previous bioconductor release (1.4)? If one is...existing installation of R-1.9.1. The downloaded getBioC() funct…

updated 21.1 years ago • Marion Hakanson

per array have an A-value located between 7 and 8. 2) It seems as there are also quite large numbers of differentially expressed probes when considering the raw per-probe p-values from the moderated t-test for the...different time-points and the p-values for the moderated F-statistic after MHC (FDR, BH). Numbers of significant probes with raw per-probe p-value < 0.05 from moderated t-tes…

Normalization Cancer limma PROcess Normalization Cancer limma PROcess

updated 18.2 years ago • Serge Eifes

hello all In the edgeR package? the lib.size: vector of length ncol(counts) giving the total number of reads sequenced for each sample. If not separately provided, will be set to colSums(counts). but there are three different...concepts. usually the number of mapped reads < total reads < counts because not all of the reads can be mapped and one mapped reads have more than

edgeR edgeR

updated 14.0 years ago • wang peter

a bit... so it's attractive, and my feeling is that it shouldn't be too problematic to reduce teh number of probes per gene to this level... but it's just a "feeling", having little experience on this type of arrays. Any thoughts...UK -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. </div

GO GO

updated 17.4 years ago • J.delasHeras@ed.ac.uk

stringtie" option and also not the none option: Is there any way to install tximport newer version or any other way. txi <- tximport(files, type = "stringtie", tx2gene = tx2gene) Error in match.arg(type, c("none", "salmon", "sailfish...setting value version R version 3.4.4 (2018-03-15) os Ubuntu 18.04.1 LTS s…

tximport stringtie RNA-seq analysis

updated 7.0 years ago • Mithil Gaikwad

recently acquired some affymetrix CEL files, with genechip Human Transcriptome Array 2.0 in order to identify possible alternative splicing events. As I'm fresh in R and Bioconductor, any tutorials or papers i have found focused

affymetrixchip GenechipHumanTranscriptomeArray2.0 exon array analysis

updated 10.7 years ago • svlachavas

<div class="preformatted">Dear list, At the moment to know the latest version of a package in the release branch I am parsing the html of the page (http://bioconductor.org/packages/release/bioc/html...div class="preformatted">Dear list, At the moment to know the latest version of a package in the release branch I am parsing the html of the page (http://bioconductor.org/packages/release…

updated 15.7 years ago • Pierre-Yves

I am trying to use Ensembl archive version via BiomaRT, below is my code ``` ensembl = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host = "oct2014.archive.ensembl.org

annotation biomart

updated 5.1 years ago • raakesh_7111

the same. (no FDR genes with the first approach vs plenty with the second) I am wondering if the number of controls "masks" the difference I could identify between A and B when it is considered in the dispersion. In this case

DESeq2

updated 3.0 years ago • andree-anne

more about which methods you used to do "After sequencing, expression was quantified by counting the number of unique molecular identifiers (UMIs) mapped to each gene." We would like to analyze as a set of data from this GEO "https

STRT-Seq single-cell tutorial

updated 5.4 years ago • tiphaine.martin

I opted to use 'method=nestedF' instead of 'method=separate', which, if I understand correctly, will identify the contrast in which a gene is deemed significant after the moderated F-tests (that subsequently will reduce the...number of multiplicity adjustments that I have to do). What is your opinion regarding my approach? Thank you for your response

limma anova decidetests

updated 7.2 years ago • mikhael.manurung

database_version* parameter of the *regulondb()* constructor function would be used to specify what version of the database one wanted to use. However, upon closer inspection of [the source code][2] I noticed that *database_version...always looks for regulondb v10.8** and there is no way for the user to specify a different version. This goes to the point that, if *connect_database()* cannot find …

regutools

updated 3.4 years ago • a.giachino2

Dear all; I recently upgraded my R to version 3.2.0, and since then I can't install the package "GenomicFeatures". I get the following warning: _Warning in install.packages...nbsp; package ‘GenomicFeatures’ is not available (for R version 3.2.0)_   Neither of I use install.packages("GenomicFeatures"), nor with biocLite("GenomicFeatures"). And therefore

genomicfeatures

updated 10.5 years ago • jcotignola

Hi I'm trying to use NanoStringDiff to analyse some Nanostring miRNA data. I am using the latest Bioconducter release (3.9) and R version 3.6. My data is in a csv file. I am going to perform differential expression analysis to identify potential biomarkers. Here is a section of my datasheet: ``` CodeClass Name Accession Epi_FAM1.1 Epi_FAM1.2 Epi_FAM2 Epi_FAM3 Posit…

NanoStringDiff

updated 6.6 years ago • noelleenright

Hello there. I am trying to use biomart to load the mouse genes for version M28 (ensembl 105), but I am getting an error: ``` ensembl_gene_names <- useEnsembl(biomart = 'genes', dataset = 'mmusculus_gene_ensembl...version = 105) Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [dec2021.archive.ensembl.org:443] Operation...timed out after 60001 millisec…

biomaRt

updated 23 months ago • RC

Hi, I am trying to use CRLMM for copy number analysis and genotyping of some human cancer samples on a Illumina 550K SNP chip. Can I used the CRLMM package for this

illumina copynumber crlmm

updated 10.1 years ago • stuti.agrawal

Hi, I was wondering if it exists an annotation package for Affy 133plus2 reporting the number of synonymous & non synonymous changes for the genes on the array. If it does not exist does anybody has a good suggestion

Annotation affy Annotation affy

updated 18.7 years ago • marco zucchelli

Hello, I wonder why, in the results of enrichGO(), the total number of genes mentionned in GeneRatio is different from the number of genes in my input?   In one analysis, I have 858 ENTREZID

clusterProfiler

updated 9.1 years ago • Jane Merlevede

I installed the latest version of R (R version 3.4.1 (2017-06-30) -- "Single Candle"), Bioconductor, and cummeRbund Platform: x86\_64-apple-darwin15.6.0 (64...I installed the latest version of R (R version 3.4.1 (2017-06-30) -- "Single Candle"), Bioconductor, and cummeRbund Platform: x86\_64-apple-darwin15.6.0 (64-bit) Mac OS X 10.11.6 I've seen posts of similar problems in the last few days.…

cummeRbund

updated 8.2 years ago • mmateos

div class="preformatted"> Hi, I need a pointer to install topGO on R version 2.14.0 Any help ... Thanks -- output of sessionInfo(): >install.packages("topGO") Installing package(s) into ???/home/gabriel...lib??? is unspecified) Warning in install.packages : package ???topGO??? is not available (for R version 2.14.0) -- Sent via the guest posting facility at bioconductor.org. <…

topGO topGO

updated 13.8 years ago • Guest User

Hello, I have a very simple question: how can I check my version of an installed package - in this case DiffBind? I know a simple `-v` in Unix achieves this, but I can't seem to figure it out...Hello, I have a very simple question: how can I check my version of an installed package - in this case DiffBind? I know a simple `-v` in Unix achieves this, but I can't seem to figure it out in R. …

DiffBind

updated 4.9 years ago • bertb

category="c3")) I want to convert this GeneSetCollection object into a list with names identifying gene sets and each entry of the list containing the gene identifiers of the genes forming the corresponding...converting a GeneSetCollection to a list. Thank you very much. Wendy [[alternative HTML version deleted]] </div

convert convert

updated 14.1 years ago • Wendy Qiao

div class="preformatted">Is there a way to display gene names as opposed to affymetrix identifiers on the y axis of a heatmap? [[alternative HTML version deleted]] </div

updated 15.3 years ago • Dave Bridges

div class="preformatted">Hi, I am using R 2.0.0 version. Do I need to update to R 2.0.1? How could I keep my R as the latest version? I downloaded R 2.0.1 tar file. Do you have to remove...the old version and reinstall the new version? In that case, I need install all the packages I installed for the old R. Do you have a better...simple way? Thanks a lot! Yanqin ---------------------------…

updated 20.7 years ago • Yanqin Yang

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

GO clusterProfiler

updated 16 months ago • Danté

Hello, I need to install an old version of DESeq2 and apeglm from 2019 in order to replicate some old results. I have tried to create a docker image using script

apeglm Install DESeq2 version

updated 4 months ago • Asma

Using the Affy cdf, I got ~2000 sig. genes, which APM ~1000. If I choose only those EntrezGene identifiers present on both cdfs, my number sig. with the APM cdf was ~1000 and there was a 90% overlap with the Affy sig. list. My conclusion...solely from APM. My conclusion from this latest observation is that APM is not annotating a large number of genes/transcripts that are in fact real. Assuming …

GO rat2302 cdf affy qvalue GO rat2302 cdf affy qvalue

updated 17.6 years ago • Mark W Kimpel

in <code><strong>1.8</strong></code>, which isn't available in bioconductor and the development version is`` ``__`` 1.7.13 ``.__ It would be useful if that guide adds some info regarding the `` tximport `` version used to carry out all...try installing from github, but i wanted to know what is the preferred way to get the last stable version of this package. Cheers &am…

tximport stringtie

updated 7.6 years ago • matrs

Hello! I'm using R version 4.0.3 (2020-10-10). I was trying to download HiCDCPlus on BiocManager, however I faced this error: ``` > BiocManager::install...HiCDCPlus") Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'HiCDCPlus' Installation path not writeable, unable...codetools, KernSmooth, nlme Warning message: package ‘HiCDCPlus’ is not ava…

HiC-DC+ HiCDCPlus BiocParallel

updated 4.8 years ago • Tay

positions on newer genome versions or > even different genomes from related species. > > The function AnalyzeTilingCel Files appears to output...the probe > intensity values - one probe per row - but it appears to create a new > identifier for each probe instead of using the x and y coordinates > from the array. > > For example, here is an e…

Microarray probe PROcess genomes Microarray probe PROcess genomes

updated 15.9 years ago • Charles Danko

by writing this email I will save other people the time I've spent on it. The problem was with the version of affyio that was being loaded. The information on the website about how to download Bioconductor does not mention...affyio. What happened was that version 1.6 was automatically found, but packages such as affy require version 1.8 or higher. Presumably this is some problem

affy affyio affy affyio

updated 17.5 years ago • Kim Evans

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

limma limma

updated 20.3 years ago • Lourdes Peña Castillo

and the counts have been generated using the dexseq\_counts.py script. However, the total number of exon for most of the genes are greater than what has been reported in literature. e.g. SNCA, which is reported to have

dexseq exons grch37

updated 8.7 years ago • aditi

have tried several gapAllowed values, 5, 500 , 5000 and 50000 .Each time I used the MCR function to identify the minimum regions. I have put an example of each results only on 25 lines of chromosome 4 to avoid massive sized...Another point, the gapAllowed is specified " is an integer specifying low threshold of base pair number " is the unit in base pair number, in several examples it seems that …

DNAcopy cghMCR DNAcopy cghMCR

updated 13.9 years ago • nac

Hello, I am trying to run a GO analysis on a set of genes I identified, but I am getting an error. Does anyone have any ideas? Thank you so much in advance! ```r library(org.Mm.eg.db) library...Function, "CC" for Cellular Component) allGenes = gene_interest, nodeSize = 10, # The minimum number of genes in a GO term annot = annotations ) ################################### …

topGO scRNAseq

updated 2.4 years ago • Francesco

gt; > > > stop("Tcl/Tk support is not available on this system") > > In previous versions of RedHat Linux, all you needed to get > R-Tcl/Tk support was the tcl and tk RPMs (RedHat packages), > whereas from RedHat...when I tried using makecdfenv to create the new CDF package, I get a Segmentation fault. I'm using R Version 1.9.0 (2004-04-12) on UNIX…

Microarray Pharmacogenomics Annotation GO Cancer cdf probe affy makecdfenv limma annaffy

updated 21.3 years ago • Mayte Suarez-Farinas

have exome and whole genome files so its a lot of resources to have them duplicated. Is there a b37 version package or a conversion workflow/tool? Many thanks, Michele [[alternative HTML version deleted]] </div

Gviz Gviz

updated 11.3 years ago • mehaffey

tried to install tximport, but received the message: "package ‘tximport’ is not available (for R version 3.2.3)". System data: Ubuntu 16.04.6 LTS, With R version 3.2.3 I have searched in the following 3 but I could not find which...R version**s** can be used with this package (though I might have missed it): 1. https://www.rdocumentation.org/packages/tximport...versions/1.0.3/topics/tx…

tximport package R version install tximport

updated 5.3 years ago • harelarik