User: Ben Mansfeld

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Posts by Ben Mansfeld

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Comment: C: Trying to account for gene length in topGO analysis
... Bernd, Thanks for your advice and explanations.  After talking to my PI and discussing the matter I think we will opt to go with matching based on average gene expression as you originally described (not the counts matrix). We also thought of using the two variables (expression and length), as you ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: Trying to account for gene length in topGO analysis
... Bernd thanks for your great detailed answer. I had looked into using the variance stabilized count matrix or even the counts(dds, normalized =T) matrix to use in genefinder and this is where I started to think that I would be getting inappropriate matches for the background. For example, I am inter ...
written 3.0 years ago by Ben Mansfeld0
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Trying to account for gene length in topGO analysis
... Hello all, I've attempted to use GOseq, and while I know that, due to the gene length correction, it is more appropriate for RNAseq data than topGO, I like that topGO takes the topology of the GO graph in to account. I'm trying to find a middle ground. In his great great tutorial (http://www-huber ...
topgo goseq deseq2 written 3.0 years ago by Ben Mansfeld0 • updated 3.0 years ago by Bernd Klaus550
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Answer: A: 10 multiple comparisons in DESeq2
... Q1: I think Relevel-ing is good so that you are at least certain what your base level is. Since you are using specific contrast that might not be an issue. If you were to just ask for results(dds), then making sure you knew what your base level was would be important. I may be wrong about this thoug ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: goseq: not able to limit by GO categories when using wallenius approximation for
... Thanks for the quick reply.  I wonder then why while using a supported genome, filtering by ontology is done in the goseq function which comes after the pwf function. Does nullp even take the GO in to account? I wasn't suggesting filtering the genes by ontology, rather subsetting the results of gos ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: goseq: not able to limit by GO categories when using wallenius approximation for
... Would it make sense to run the analysis with all terms (including all groupings) then filter them afterwards, just before the multiple testing? Or will this affect anything statistically? ie: GO_Age_dwn<-goseq(pwfAge_dwn, gene2cat = CukeGO) GO_Age_dwn_BP<-subset(GO_Age_dwn, ontology == "BP" ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after p
... Hervé, Thanks for addressing this. I couldn't figure it out for the life of me. I appreciate all the work you devs do! -Ben ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after p
... Thanks for the reply. Sorry about that. Here are a few lines from the top: Chr1 . gene 2952 4284 . - . ID=Csa1G000010; Name=Csa1G000010 Chr1 . mRNA 2952 4284 . - . ID=Csa1M000010.1; Parent=Csa1G000010; Name=Csa1M000010.1 Chr1 . five_prime_utr ...
written 3.0 years ago by Ben Mansfeld0
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Comment: C: GOSeq: analysis of unsupported genome after HTseq and DEseq2 - building gene len
... Thanks for the reply. That's what I guessed. Do you think this makes a difference to the analysis?  Does fitting to the PWF still work if DE goes down with size? Is GOseq still a valid approach for my purposes? Thanks again ...
written 3.0 years ago by Ben Mansfeld0
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makeTxDbFromGFF Error: subscript contains NAs or out-of-bounds indices - after package update
... Hello all,  I appreciate any help in advance. This has been driving me crazy for the last 24hrs... I am trying to extract exon lengths from my GFF3 file.  txdb <- makeTxDbFromGFF("../../Chinese Long Genome/cucumber_v2.gff3",format="gff3") exBytx<-exonsBy(txdb, by="tx", use.names=T) txlengt ...
genomicfeatures written 3.0 years ago by Ben Mansfeld0 • updated 3.0 years ago by Hervé Pagès ♦♦ 14k

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