User: Johnny H

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Johnny H80
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Posts by Johnny H

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Answer: A: RNAseq, what to do if you have no replicates in voom-limma
... Thank you very much for that. It really is a good idea, which gives a balance between saving money and still having biological replicates, albeit fewer reads per rep. I have passed this idea on to the people who make the decisions.    ...
written 3.8 years ago by Johnny H80
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Answer: A: RNAseq, what to do if you have no replicates in voom-limma
... Thank you for your answer and a solution to this.  Yes you are obviously right in this situation, we don't need to look at the pooled samples.  The reason we are looking at this approach, as can often be the case, is money. We have many conditions to look at, and to do 3 biological replicates of a ...
written 3.9 years ago by Johnny H80 • updated 3.8 years ago by Gordon Smyth37k
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RNAseq, what to do if you have no replicates in voom-limma
... Dear Limma/EdgeR users, I have 2 treatment groups, 3x biological replicates for each. I also have 2 extra samples, a pool of each treatment group.  I am comparing a "vanilla" analysis with the biological replicates, to an analysis with the pooled samples. I.e 1 vs. 1 sample. In the EdgeR manual, ...
limma edger voom written 3.9 years ago by Johnny H80 • updated 2.7 years ago by Konika Chawla20
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Comment: C: How is fold change reported in the samr output?
... Hi James thanks for the answer, :-) Perl is not so bad With my data, I get this.... colnames(siggenes.table$genes.lo) [1] "Row" "Gene ID" "Gene Name" "Score(d)" [5] "Numerator(r)" "Denominator(s+s0)" "q-value(%)" Did I run SAMR in the wrong manner? On Tue, Sep 14, ...
written 8.7 years ago by Johnny H80
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Comment: C: Using linear models to find differential gene expression (NGS)
... Dear Simon, Naomi and Kasper, Thank you very much for your detailed answers and suggestions. It is very helpful. Simon, it is very interesting how you describe the example. From what I understand; I should use a negative Binomial statistic (your DESeq or EdgeR) that accounts for biological variatio ...
written 8.7 years ago by Johnny H80
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Using linear models to find differential gene expression (NGS)
... Hi. I have found some R/Bioconductor/Genominator code on the web (below) and it measures differential expression of RNA-seq short read data using a general linear model. Can someone explain some basic questions I have? 1) What is the reason for using 2 glm's for measuring differential expression? ...
written 8.7 years ago by Johnny H80 • updated 8.7 years ago by Thomas J Hardcastle180
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Fwd: Genominator problem
... http://www.bioconductor.org/help/course- materials/2009/SeattleNov09/RNASeq/RNASeqTools.pdf This is the document I found on the web. It is interesting as it has some functions to perform the Bullard et al. UpperQuartile normalisation. I want to see how that transforms transcript counts, hence me car ...
genominator written 8.7 years ago by Johnny H80
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Comment: C: Genominator problem
... Thanks Kasper for that, the command works but... > yAnnoUI <- makeGeneRepresentation(yAnno, type = "UIgene") Error: transcript.id %in% names(annoData) is not TRUE > annoData Error: object 'annoData' not found Where is annoData coming from? On Fri, Aug 27, 2010 at 2:59 PM, Kasper Daniel Ha ...
written 8.7 years ago by Johnny H80
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Genominator problem
... Dear Bioconductors, I am using the Genominator library and work through the example...until I get to here > yAnnoUI <- Genominator:::makeUIgenes(yAnno, gene.id = "ensembl_gene_id", transcript.id = "ensembl_transcript_id", verbose = TRUE) Error in get(name, envir = asNamespace(pkg), inherits = ...
genominator written 8.7 years ago by Johnny H80 • updated 8.7 years ago by Kasper Daniel Hansen6.4k
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Comment: C: PCA or concordance
... Dear Steve and Sean. First, thanks for replying to my query. Normalisation: Yes, I will normalise to number of peptides per gene model (due to isoforms). If I wanted to be ultra careful, I would see if any peptides were specific to any one isoform but that is complicated and probably inaccurate. ...
written 9.2 years ago by Johnny H80

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For RNAseq, what to do if you have no replicates in voom-limma

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