User: willmacnair

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Posts by willmacnair

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Comment: C: Grouping similar genes in differential expression analysis to increase power
... Thanks for the quick response. I had a quick search for this combination (goseq then DESeq2) but couldn't see anything obvious. I'm not clear how these would be combined, but perhaps I'm missing something obvious. The approach I'm thinking of would be something like: - group all measured genes into ...
written 3.8 years ago by willmacnair0
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Grouping similar genes in differential expression analysis to increase power
... Hi I've recently done some DE analysis with DESeq2, with relatively small sample sizes. The experimental setup is a time course of 4 points, with matched samples of two different tissue types from 7 patients (so 56 samples in total). I've tested t3 against t0 in both tissue types. Since I expect th ...
rnaseq deseq2 differential gene expression written 3.8 years ago by willmacnair0 • updated 3.8 years ago by Michael Love26k
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Answer: A: topGO annotations issue
... OK, thanks for trying to help! I think what you've now suggested was what I was originally doing in the example I posted - I'd previously had success using gene_vector as a boolean vector, converted to a factor, but with a different chip. Thanks for the suggestion of GOstats. I'll try anything whic ...
written 4.8 years ago by willmacnair0
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Comment: C: topGO annotations issue
... So I have now tried GOdata_BP = new("topGOdata", ontology = 'BP', allGenes = gene_universe, geneSel = gene_vector, annotationFun = annFUN.db, affyLib = affy_library ) however I get the following error: Error in .local(.Object, ...) : a ...
written 4.8 years ago by willmacnair0
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topGO annotations issue
... Hi I am trying to run a GO enrichment test on genes identified in experiments on an  affymetrix hgu133plus2 chip. I get zero annotations, even though within hgu133plus2.db  I can find annotations for the genes of interest. I've spent a while trying to get it to work but with no success. What (no dou ...
topgo annotationdbi written 4.8 years ago by willmacnair0
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Comment: C: Incomplete gene IDs in KEGG pathway testing
... Hi James Thanks for your response. I now have a more up-to-date way of obtaining Entrez Gene IDs, but this doesn't solve the problem of incomplete annotation in illuminaHumanv3.db (i.e. even using select, the genes I chose as having NAs still have NAs). Do you have any suggestions for solving this? ...
written 4.9 years ago by willmacnair0
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Incomplete gene IDs in KEGG pathway testing
... I am trying to do pathway enrichment analysis for a set of genes from an Illumina chip, and I'm having problems with using hyperGTest (from the GOstats package).  My approach is: define gene_list and gene_universe in the same format, in this case using the Illumina gene identifiers (e.g. ILMN_177 ...
gostats kegg written 5.1 years ago by willmacnair0 • updated 5.1 years ago by James W. MacDonald52k

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Popular Question 3.7 years ago, created a question with more than 1,000 views. For topGO annotations issue

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