rna-seq

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Hi everybody, I Have used goseq to take out the enriched GO-terms from my RNA-seq and microarray data and I want to visualize the output from goseq in a network since it is just a list of GO-terms and I cannot see an overview of my result. So my question is what package or software should I use to see a network of regulated GO-terms or pathways. Regards, Saman -- output of sessionInfo(): R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] edgeR_2.6.12 limma_3.12.3 goseq_1.8.0 [4] geneLenDataBase_0.99.9 BiasedUrn_1.04 loaded via a namespace (and not attached): [1] AnnotationDbi_1.18.3 Biobase_2.16.0 BiocGenerics_0.2.0 [4] biomaRt_2.12.0 Biostrings_2.24.1 bitops_1.0-4.1 [7] BSgenome_1.24.0 DBI_0.2-5 GenomicFeatures_1.8.3 [10] GenomicRanges_1.8.13 grid_2.15.0 IRanges_1.14.4 [13] lattice_0.20-10 Matrix_1.0-9 mgcv_1.7-21 [16] nlme_3.1-104 RCurl_1.91-1 Rsamtools_1.8.6 [19] RSQLite_0.11.2 rtracklayer_1.16.3 stats4_2.15.0 [22] tools_2.15.0 XML_3.9-4 zlibbioc_1.2.0 -- Sent via the guest posting facility at bioconductor.org.

Microarray Pathways Network goseq Microarray Pathways Network goseq • 1.2k views

ADD COMMENT • link updated 12.3 years ago by Aliaksei Holik ▴ 350 • written 12.3 years ago by Guest User ★ 13k

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Aliaksei Holik ▴ 350

@aliaksei-holik-4992

Last seen 8.9 years ago

Spain/Barcelona/Centre for Genomic Regu…

Dear fellow Bioconductors, I'm faced with a problem I can't get my head round and hope somebody would be able to point me in the right direction. I am trying to plot a heatmap using expression values from my array for an external set of genes. I have used illuminaMousev2ALIAS2PROBE object to extract IlluminaIDs corresponding to the gene symbols in the set. Consistent with possibility of more than 1 probe per gene I got 1052 IlluminaIDs for 510 gene names. However, if I try to remove duplicates I only get 259 IlluminaIDs, which makes no sense to me. I have checked and I do indeed get a lot of duplicated probe IDs. I wonder where I go wrong. Here's the code I used: # Generate a list of gene symbols with corresponding Illumina IDs xx <- as.list(illuminaMousev2ALIAS2PROBE) # Subset all Illumina IDs for the genes present in SCSGenes vector scs.probes.and.genes <- xx[SCSGenes] # Generate a vector of probes while removing gene names scs.probes <- as.character(unlist(scs.probes.and.genes)) #1058 probes scs.probes <- na.omit(scs.probes) #1052 probes # Remove duplicates scs.probes <- scs.probes[!duplicated(scs.probes)] #259 probes # end of code Any help is much appreciated. All the best, Aliaksei.

ADD COMMENT • link 12.3 years ago Aliaksei Holik ▴ 350

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Before anyone replies, I just had an idea that I should try illuminaMousev2SYMBOL instead of illuminaMousev2ALIAS2PROBE. If I fail, in that I'll send another e-mail. Thanks again. On 27/09/2012 17:05, Aliaksei Holik wrote: > Dear fellow Bioconductors, > > I'm faced with a problem I can't get my head round and hope somebody > would be able to point me in the right direction. > > I am trying to plot a heatmap using expression values from my array for > an external set of genes. I have used illuminaMousev2ALIAS2PROBE object > to extract IlluminaIDs corresponding to the gene symbols in the set. > Consistent with possibility of more than 1 probe per gene I got 1052 > IlluminaIDs for 510 gene names. However, if I try to remove duplicates I > only get 259 IlluminaIDs, which makes no sense to me. I have checked and > I do indeed get a lot of duplicated probe IDs. I wonder where I go > wrong. Here's the code I used: > > > # Generate a list of gene symbols with corresponding Illumina IDs > xx <- as.list(illuminaMousev2ALIAS2PROBE) > # Subset all Illumina IDs for the genes present in SCSGenes vector > scs.probes.and.genes <- xx[SCSGenes] > > # Generate a vector of probes while removing gene names > scs.probes <- as.character(unlist(scs.probes.and.genes)) #1058 probes > scs.probes <- na.omit(scs.probes) #1052 probes > > # Remove duplicates > scs.probes <- scs.probes[!duplicated(scs.probes)] #259 probes > # end of code > > Any help is much appreciated. > > All the best, > > Aliaksei. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > >

ADD REPLY • link 12.3 years ago Aliaksei Holik ▴ 350

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Dear Pan and fellow Biocondictors, I am trying to generate a file for submission to GEO database. However, when trying to generate a Template File I'm confronted by the following error: > produceGEOSampleInfoTemplate(normalised.data, lib.mapping=lumiMouseIDMapping, fileName="GEOTemplate.txt") The input object should be an object of LumiBatch, MethyLumiM, matrix or other ExpressionSet inherited class! Error in templateContent[templateTitle == "Sample_data_processing"] <- preprocessMethod : object 'templateContent' not found The normalised.data file has been produced using beadarray package and has the following class: > class(normalised.data) [1] "ExpressionSetIllumina" attr(,"package") [1] "beadarray" I understand, this would qualify it as an ExpressionSet inherited class and I'm at loss, why it isn't recognised by produceGEOSampleInfoTemplate. Any help would be much appreciated, Aliaksei. P.S. My sessionInfo output and lumi loading messages: > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 [3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] lumi_2.8.0 nleqslv_1.9.4 methylumi_2.2.0 BiocInstaller_1.4.7 [5] ggplot2_0.9.2.1 reshape2_1.2.1 scales_0.2.2 Biobase_2.16.0 [9] BiocGenerics_0.2.0 loaded via a namespace (and not attached): Error in x[["Version"]] : subscript out of bounds In addition: Warning message: In FUN(c("affy", "affyio", "annotate", "AnnotationDbi", "bigmemory", : DESCRIPTION file of package 'RSQLite' is missing or broken > library(lumi) Loading required package: methylumi Loading required package: nleqslv bigmemory >= 4.0 is a major revision since 3.1.2; please see package biganalytics and http://www.bigmemory.org for more information. KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: ?lumi? The following object(s) are masked from ?package:methylumi?: estimateM, getHistory Warning messages: 1: replacing previous import ?image? when loading ?graphics? 2: package ?nleqslv? was built under R version 2.15.1 3: replacing previous import ?density? when loading ?stats? 4: replacing previous import ?residuals? when loading ?stats?

ADD REPLY • link 12.3 years ago Aliaksei Holik ▴ 350

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