Hi, On 02.01.2017, I ran an analysis with DESeq2. I ran a similar analysis recently. I used the same input data for both runs! Please see "raw reads" in the excel file ([https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2\_bugreport\_23102017.xlsx?dl=0](https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2_bugreport_23102017.xlsx?dl=0)). Even tough the normalized reads and basemean are same in both runs…

other attached packages: \[1\] DESeq2\_1.10.0 RcppArmadillo\_0.6.200.2.0 Rcpp\_0.12.1 qvalue\_2.2.0 goseq\_1.22.0 geneLenDataBase\_1.6.0 BiasedUrn\_1.06.1 WGCNA\_1.48 RSQLite\_1.0.0 \[10\] DBI\_0.3.1 fastcluster\_1.1.16

genes belong to specific gene ontologies to infer different functions between my groups. I used goseq package to make GO analysis and finally obtained the list of significatively over-represented GO with their associated

Hi all, I'm using PANTHER.db to run some enrichment analysis and am trying to use the function pthOrganisms to restrict the database to mouse.  More specifically, the code is: pthOrganisms(PANTHER.db) = "MOUSE" However, I obtained the following error: Error: could not find function "pthOrganisms" The package installs just fine and the library loads correctly.  Page 3 of the…

of package ‘minfi’ had non-zero exit status 31: In .inet_warning(msg) : installation of package ‘goseq’ had non-zero exit status 32: In .inet_warning(msg) : installation of package ‘methylumi’ had non-zero exit status 33: In .inet_warning

tons of tools supporting GO such as >>>>>> GO.db, >>>>>> topGO, goseq, GOstats, biomart etc... and I have been reading their >>>>>> description and examples, but honestly I am overhelmed

RaExExonProbesetLocation", "snow", "RmiR", "RmiR.Hs.miRNA", "R.utils", "EDASeq","DESeq", "DEXSeq","goseq", "BSgenome.Hsapiens.UCSC.hg19", "TxDb.Hsapiens.UCSC.hg19.knownGene", "oneChannelGUI","chimera", "cummeRbund")) I could

I am trying to make an organism db to use with GoSeq for pancium hallii. Using the biomart package I found what dataset to use but I get the error that 0 or more than 1 subdir

Previously, I invoked runValue (strand (GRangesList)) in order to extract strand information for a GRangesList object. However, upon updating to R 3.1.2 and Bioconductor 3.0, this code no longer works: >   refSeqDb = suppressWarnings (makeTranscriptDbFromUCSC (     "hg19",     tablename = "refGene")) > h…

Re: displaying the image with EBImage (Nima Ahmadian) 21. Re: Negative parameter error when using goseq (Nadia Davidson) 22. Re: anova like test in edgeR (Gordon K Smyth) 23. Re: Subsampling of BAM/SAM alignments (Martin Morgan) 24

Dear all, We still have a few seats available for our upcoming online course: Gene Set Enrichment Analysis in R/Bioconductor, in March (3-6). Course website: https://www.physalia-courses.org/courses-workshops/gse-in-r/ In this course, we will teach the use of popular GSEA tools, both for online-based tools and those implemented as R packages. We will give a detailed introduction to a var…

Hi I have a list of differentially expressed genes for E.coli (BL21). Now with this genes I would like to do some downstream analysis. Can you guys help me out with some ideas? I tried to do some functional enrichment analysis but I dont have any ENTREZ id. How can I tackle this problem

Hi, I am trying to do GO enrichment analysis. I work on Cannabis sativa, which is a non-model organism. There are no GO terms for Cannabis, so I cannot make use of the orgdb or biomart functions in R. However, I have generated a file with GO terms mapped to protein id from the original fasta. My file looks like this: ```r !db db_object_id db_object_symbol qualifier …

Hi, I'm trying to use PANTHER.db to conduct pathway analysis on a set of differentially expressed genes, and I'm running into an error when loading PANTHER.  I install as usual:

biocLite("PANTHER.db")
library(PANTHER.db)

But when I type PANTHER.db at the console, I obtain the following error:

Error in rsqlite_send_query(conn@ptr, statement) :
  external pointer is not valid

This e…

Hi, I found the below code [here](https://www.biostars.org/p/84467/#84495): > library(GenomicRanges) > library(rtracklayer) > library(Rsamtools) Loading required package: Biostrings Loading required package: XVector > > GFFfile = "snap_augustus.gff" > FASTAfile = "genome_29155.faa" > > #Load the annotation and reduce it …

Hello I am using go-seq for gene enrichment study. I am having few confusion I will be very grateful if I can get some help. 1) I know we need gene length to calculate the bias. 2) I want to do gene enrichment of two groups compared to the control group. - i got a list of transcripts which are commonly differential expressed in both theses group(A, B) against the control group. - …

Hello -I am using Go-seq for my gene enrichment study. - I have my pwf test file which look like below. This file has protein ID as row names. - My question in order to do mapping between the two files, do I need to select column from the GAF format file. and then split the column, to get the protein id name so that I can further do mapping. Looking forward to hearing, and thanks for …