bioconductor@r-project.org discussions

0	[BioC] Important announcement about our new support site

Hello! We are pleased to announce the official transition to our new support site, https://support.bioconductor.org This site replaces the Bioconductor mailing list as the primary source for user ...

Marc Carlson
Sep 15, 2014 at 10:40 pm
Sep 15, 2014 at 10:40 pm

0	[BioC] design matrix in limma

Hello BioC forum, I am making a design matrix for gene expression data analysis with the adjustment of Sex variable. The R code I am using is below. I want to make sure if I am doing correctly ...

KC [guest]
Sep 15, 2014 at 9:24 pm
Sep 15, 2014 at 9:24 pm

0	[BioC] PI position at EMBL-EBI (Cambridge UK)

// see https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jj&idR950&aid470 which can also be reached from the EMBL / Jobs homepage. We are seeking an outstanding computational biologist to establish a ...

Wolfgang Huber
Sep 15, 2014 at 5:36 pm
Sep 15, 2014 at 5:36 pm

1	[BioC] affymetrix probe databases

Good afternoon to everybody, I'm just doing my firsts steps working with affymetrix data and i have some questions. I started to working with CEL files by moving the data contained in them to a csv ...

Pau Marc Muñoz Torres
Sep 15, 2014 at 2:40 pm
Sep 15, 2014 at 3:33 pm

5	[BioC] Course: Learning R / Bioconductor for Sequence Analysis, Seattle, WA Oct 27-29

Course: Learning R / Bioconductor for Sequence Analysis Dates: October 27-29, Seattle, WA. Registration: https://register.bioconductor.org/Seattle-Oct-2014/ This course is directed at beginning and ...

Martin Morgan
Sep 15, 2014 at 2:13 pm
Sep 15, 2014 at 8:53 pm

2	[BioC] Interaction categorical/continuous variable DESeq2

Dear list, dear Mike Love, I am using DESeq2 to model counts from an unusual type of experiment and I have a question about the strategy I employed. The experiment consisted in sequencing 33 samples ...

Hugo Varet
Sep 15, 2014 at 1:41 pm
Sep 15, 2014 at 5:54 pm

0	[BioC] NA values in Biomart query

Hi, I want to retrieve some annotation informations from "ensembl exon id" by using a biomart query : "ensembl gene id", "ensembl transcript id", ... After my "getBM" query, without error message, my ...

Chapeaublanc Elodie
Sep 15, 2014 at 11:23 am
Sep 15, 2014 at 11:23 am

0	[BioC] error: "'names' attribute [16] must be the same length as the vector [2]", using Making Organism packages use of makeOrgPackage()

I am creating my annotation package using makeOrgPackage(). I followed the instruction here ...

Stefano romano
Sep 15, 2014 at 8:46 am
Sep 15, 2014 at 8:46 am

2	[BioC] export funciton alters ranges in output BED file

Hello I am attempting to use the export() function to generate a BED file from a GRanges object. However, the ranges in the output file are altered so that the start coordinate is subtracted by one, ...

Do r
Sep 14, 2014 at 2:42 pm
Sep 14, 2014 at 7:20 pm

1	[BioC] DE analysis of PCR array [was: dataset dim for siggenes]

Hi Fred, We frequently use limma to analyze ct values from PCR arrays similar to yours (although usually with fewer samples), so the analysis that you have already done is basically what we ...

Gordon K Smyth
Sep 14, 2014 at 3:22 am
Sep 14, 2014 at 4:54 am

3	[BioC] HGU133Plus2 CDF vs hgu133plus2hsentrezgcdf CDF (30% difference in results)

Hello, My name is Mahes Muniandy and I am a doctoral student. I have been analysing Affymetrix HGU133Plus2 cel files to determine differential expressions in twin pairs (within pair differences). I ...

Mahes Muniandy [guest]
Sep 13, 2014 at 6:31 pm
Sep 15, 2014 at 10:30 pm

0	[BioC] Bioinformatics researching Schizophrenia

I am an undergraduate student and I have been given a project that involves bioinformatics. My supervisor researches chromosome abnormalities and gene expression and he has been given a list of GWAS ...

Chris Clarkson [guest]
Sep 13, 2014 at 12:56 pm
Sep 13, 2014 at 12:56 pm

1	[BioC] Ask help for Rcpp

Does anyone know how to use regex in Rcpp for Bioconductor package development? Best regards! Bo -- output of sessionInfo(): No -- Sent via the guest posting facility at bioconductor.org.

Bo [guest]
Sep 13, 2014 at 8:29 am
Sep 13, 2014 at 12:22 pm

0	[BioC] topGO: how to visualize gene in GO enriched categories?

Hi All, I am using 'topGO package for GO enrichment analysis in non model organisms. I found the tool really intuitive and versatile as far as the statistical test are concerning. However, I was ...

Stefano romano
Sep 13, 2014 at 8:13 am
Sep 13, 2014 at 8:13 am

2	[BioC] KEGGprofile: "Error in phyper - Non-numeric argument to mathematical function" when using non model organism

Hi, I am using KEGGprofile to perform KEGG enrichment for a non model organism. Using the data from the R documentation i perfectely obtaine the enrichment. Length Class Mode 300 character character ...

Stefano romano
Sep 13, 2014 at 8:03 am
Sep 15, 2014 at 2:50 pm

0	[BioC] important announcement

Hello, This is a second warning that in less than a week we plan to roll out the new support site for Bioconductor. *Important* Once the support site is 'live', posts to the Bioconductor mailing list ...

Marc Carlson
Sep 12, 2014 at 10:08 pm
Sep 12, 2014 at 10:08 pm

0	[BioC] what drives sample outliers in 450k (detectOutlier, lumi)

Hi there I am finding some sample outliers in the result from the detectOutlier method in lumi. I don?t see anything strange about these samples when I look at the mean beta values. I wonder how I ...

Victoria Svinti
Sep 12, 2014 at 7:29 pm
Sep 12, 2014 at 7:29 pm

2	[BioC] Packages for GO and KEGG analysis on RNAseq data

Dear all, We are two biologists (so very new in bioinformatic field...) working with RNAseq data and having little "troubles" with pathways analysis. We performed mRNA sequencing on 4 distinct cell ...

Merienne Nicolas
Sep 12, 2014 at 5:54 pm
Sep 12, 2014 at 7:40 pm

0	[BioC] [Bioc-devel] AnnotatioDbi Biostrings load order breaks GenomicFiles summary method

[keeping the list in the loop] These packages can go into Suggests and don't need to be in NAMESPACE. You do need to library() these packages in your test code. Dan

Dan Tenenbaum
Sep 12, 2014 at 5:18 pm
Sep 12, 2014 at 5:18 pm

0	[BioC] Changing the x axis size using tracks (ggbio)

Hello, I am using the tracks function from ggbio package, but I am unable to change the size in the x axis. The df dataframe: chr start end id chr12 72065147 72204484 ENSBTAG00000045751 chr12 ...

Vinicius Henrique da Silva
Sep 12, 2014 at 3:19 pm
Sep 12, 2014 at 3:19 pm

5	[BioC] dataset dim for siggenes

Hi list, I have a qPCR 116 x60 data set processed with limma. Results showed 30 DE miRNAs. My idea is to pick-up 10 of them for validation running further statistical tests and taking the most ...

Ferreirafm
Sep 12, 2014 at 3:18 pm
Sep 12, 2014 at 10:45 pm

0	[BioC] DiffBind annotation

Hi Igor- We avoided adding annotation to DiffBind because of the other packages that specialize in this. They don't take a DiffBind object directly, but you can always retrieve any peak set as a ...

Rory Stark
Sep 12, 2014 at 2:20 pm
Sep 12, 2014 at 2:20 pm

1	[BioC] log2 as input in limma

Hi all, I have performed batch-normalization on my RNA-Seq data leaving the data as cpm-log2 normalized. How do I use this as input in limma? It usually only take count data. -- output of ...

R [guest]
Sep 12, 2014 at 10:31 am
Sep 12, 2014 at 1:24 pm

2	[BioC] no method for coercing S4 class to a vector

Dear all, I have a similar problem to this poster here: http://grokbase.com/t/r/bioc-devel/141cegqvpf/no-method-for-coercing-this-s4-class-to-a-vector The error message is: Error in as.vector(x) : no ...

Ninni Nahm [guest]
Sep 12, 2014 at 8:27 am
Sep 12, 2014 at 1:39 pm

2	[BioC] error in report(qa) from pkg ShortRead

Hello, I have a fastq file compressed with gzip in a directory named test/. I would like to assess its quality. Here is what I do: $ R And I get the following error message: Error in ...

Timothée Flutre
Sep 11, 2014 at 3:38 pm
Sep 12, 2014 at 12:40 pm

9	[BioC] Repeat masker sequences as GRanges object

Hello, I would like to have repeat sequences as GRanges object I started with ... library (BSgenome.Hsapiens.UCSC.hg19) ch1 <- Hsapiens$chr1 active (masks (ch1)) AGAPS AMB RM TRF TRUE TRUE FALSE ...

Hermann Norpois
Sep 11, 2014 at 10:16 am
Sep 15, 2014 at 11:19 am

1	[BioC] XVector

Hi, You're not showing the command you used to install XVector. Remember that you should *always* use biocLite() to install a Bioconductor package, as explained here: http://bioconductor.org/install/ ...

Hervé Pagès
Sep 11, 2014 at 4:29 am
Sep 11, 2014 at 6:15 am

0	[BioC] how to fetch GO categories from Chinese hamster genome

Hi, I have been trying to generate GO category table for Chinese hamster genome using getgo function in goseq package. Even though chinese hamster is said to be included in the supportedGenomes() ...

Upendra kumar devisetty
Sep 10, 2014 at 6:32 pm
Sep 10, 2014 at 6:32 pm

2	[BioC] Error using Bsmooth.tstat due to NAs

Dear all, I am trying to use bsseq to analyze WGBS data and identify DMRs following drug treatment. I have a BSseq object consisting of 2 samples (treated and ctrl) that has been smoothed: An object ...

Fides Lay [guest]
Sep 10, 2014 at 4:18 pm
Sep 14, 2014 at 5:48 pm

1	[BioC] [JOB] NIH-Wide Stadtman Tenure-Track Recruitment

The National Institutes of Health is now accepting applications for tenure-track positions through the Earl Stadtman recruitment mechanism. Details are available here: http://goo.gl/vF95Pi Sean ...

Sean Davis
Sep 10, 2014 at 3:40 pm
Sep 10, 2014 at 4:34 pm

1	[BioC] Organism annotation package created with makeOrgPackage doesn't install properly

I work with the plant Sorghum bicolor and want to make my own organism annotation package. I created package with makeOrgPackage and also tried the example in ...

Lasse Nielsen [guest]
Sep 10, 2014 at 2:12 pm
Sep 10, 2014 at 3:06 pm

0	[BioC] Workshop Statistical Learning of Biological Systems - Ascona, Switzerland, May 31 to June 5, 2015

Announcement of the Workshop on Statistical Learning of Biological Systems from Perturbations in Ascona, Switzerland, May 31 to June 5, 2015 Advances in biotechnology have made genome-scale ...

Wolfgang Huber
Sep 10, 2014 at 12:17 pm
Sep 10, 2014 at 12:17 pm

2	[BioC] barcode support for other platforms

I am trying to assess whether genes in my samples are over expressed relative to a null mean. I use the barcode function in the R package frma for this purpose. As far as I understand the current ...

Romi Admanit [guest]
Sep 10, 2014 at 1:20 am
Sep 10, 2014 at 11:35 am

0	[BioC] FlowCore Question

Great! [[alternative HTML version deleted]]

Mike
Sep 10, 2014 at 12:29 am
Sep 10, 2014 at 12:29 am

1	[BioC] How to get genes within a GO category of 'GOstat' results?

Hi All, I am using 'GoStat' package for GO enrichment analysis and so far I have been able to generate results from 'hyperGTest' without any issue. Here is my dummy code: top.genes = ...

Atul
Sep 9, 2014 at 5:31 pm
Sep 9, 2014 at 6:46 pm

3	[BioC] unable to set sampleNames after combine (from beadarray package) on ExpressionSetIllumina

Dear all, Here is a possible bug in the combine() function from beadarray. I read two ExpressionSetIllumina objects with 36 samples and 12 samples each. The combine() function works brilliantly and ...

Adaikalavan Ramasamy
Sep 9, 2014 at 10:52 am
Sep 11, 2014 at 3:41 pm

1	[BioC] Gostats Hypergeometric tests for non model organisms Kegg pathway

Hello I would like to run an hypergeometric testing on KEGG terms for non-model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes ...

Claire [guest]
Sep 9, 2014 at 9:18 am
Sep 9, 2014 at 10:29 pm

7	[BioC] positively correlated genes

hi I am interested to find out the genes that are positively and negatively correlated genes with my genes of interest. (using rnaseq normalized expression data). Can some one suggest me a better ...

Karthik [guest]
Sep 9, 2014 at 8:41 am
Sep 13, 2014 at 12:40 am

1	[BioC] insertion site detection

Hi all, I need your guidance in this, I have dna sequence paired end reads with known non-reference transposable element sequence insertions (~1000 bp). I do have a reference genome. I am wondering ...

Alpesh Querer
Sep 9, 2014 at 5:13 am
Sep 9, 2014 at 6:09 am

4	[BioC] Consensus sequence

I have a use case that I am not sure the best way to proceed. I have a non-model organism for which we would like to know the sequence for a set of genes. It's a bird species, and I can for example ...

James W. MacDonald
Sep 9, 2014 at 2:32 am
Sep 12, 2014 at 5:15 pm

1	[BioC] Converting .gpr files to .csv files

I just got some microarray data sent over to me. The files are .gpr and I would like to convert then to .csv files to open the data in excel and eventually in R. Im not sure how to go about doing ...

Adriana Charles [guest]
Sep 9, 2014 at 12:38 am
Sep 9, 2014 at 2:16 am

1	[BioC] Test Statistic in nbinomialTest in DESeq???

Hi everyone, Does nbinomialTest in DESeq calculate a test statistic? According to DESeq documentation, "nbinomTest calculates a p value by summing up the probabilities of all per-group count sums a ...

Sarven Sabunciyan [guest]
Sep 8, 2014 at 4:15 pm
Sep 9, 2014 at 8:13 am

5	[BioC] Tissue heterogeneity and TMM normalization

Dear all, I have a general question about whether TMM normalization is appropriate for my data. I apologize for this long winded email. I am not a trained bioinformatician and therefore have been ...

Ni Feng
Sep 8, 2014 at 4:15 pm
Sep 9, 2014 at 5:38 pm

1	[BioC] DiffBind time course

Hi, Is there a way to use DiffBind to analyse time course data? I have sample and control replicates at five different time points and I would like to know which sites show differential binding over ...

Enrico Ferrero
Sep 8, 2014 at 11:01 am
Sep 9, 2014 at 3:20 pm

0	[BioC] Consultation about combing batches

Dear friend, I'm trying to use your ComBat R script to eliminate batch effect when combine high-throughput gene expression data from different batches. However, there is an issue about the R code ...

Shaowei Wu
Sep 8, 2014 at 2:28 am
Sep 8, 2014 at 2:28 am

5	[BioC] Motif enrichment analysis: Error in transfac format and background frequencies from BSGenome

Hi all, I am scanning a geneset for all the Mmusculus motifs and comparing their enrichment to genomic background. I am using MotifDb package to retrieve motifs and PWMEnrich for doing motif ...

Deepti anand
Sep 7, 2014 at 3:47 pm
Sep 9, 2014 at 2:06 pm

1	[BioC] Trouble installing topGO package

Hi, I've been trying to install the topGO package on Linux (debian squeeze), but I keep getting this error when installing the SparseM dependency: * installing *source* package ?SparseM? ... ** ...

Eric Fournier
Sep 5, 2014 at 5:49 pm
Sep 8, 2014 at 7:18 pm

5	[BioC] RNA-seq differentially expressed gene finding methods

Dear all, I know that we have quite very good packages (edgeR, deseq) that calculate the list of differentially expressed genes in 2 conditions (with replicates) from raw counts. But I do not know ...

Son Pham
Sep 5, 2014 at 4:44 pm
Sep 6, 2014 at 7:39 pm

4	[BioC] Access to BiocGenerics 0.11.4 package

Hello , I try to download the BiocGenerics 0.11.4 package, directly on the website: http://bioconductor.jp/packages/3.0/bioc/html/BiocGenerics.html but I have a message : Server problem. How to get ...

Gregory voisin
Sep 5, 2014 at 3:45 pm
Sep 5, 2014 at 4:41 pm

7	[BioC] HTSeq-Count

Hi all, I am new to the field of seq and performed a RIP-Seq experiment using HTSeq count as counter. I get now the following (using union, but doesn??t look better for interesection_strict) ...

Julia [guest]
Sep 5, 2014 at 2:41 pm
Sep 8, 2014 at 5:36 pm

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