User: Alicia Oshlack

gravatar for Alicia Oshlack
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Posts by Alicia Oshlack

<prev • 10 results • page 1 of 1 • next >
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Answer: A: goseq analysis
... Hi Dave, I¹d just like to mention that I don¹t believe that using gene lengths for CAGE data is the right thing to do because you are not counting the number of reads across the whole transcript, which will correlate with gene length. Therefore I believe you should not use the automatic fetching of ...
written 5.1 years ago by Alicia Oshlack100
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Answer: A: goseq/nullp with non-native identifiers
... Hi Ravi, You can use your own length data and GO categories by: pwf=nullp(gene.vector,bias.data=lengthData) go=goseq(pwf,gene2cat=GOmap) Cheers, Alicia On 3/09/12 8:00 PM, "bioconductor-request at r-project.org" wrote: > Date: Sun, 2 Sep 2012 09:39:48 -0400 > From: Ravi Karra > To: bi ...
written 5.2 years ago by Alicia Oshlack100
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Answer: A: GOseq for enrichment of clustering results
... Hi Julie, In theory you can get your list of "DE" genes any way you like before using Goseq. The issue however for GOseq is that usually when you perform a statistical test for DE it is biased towards long and highly expressed genes. I'm not exactly sure how these features will effect clustering bu ...
written 5.6 years ago by Alicia Oshlack100
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Answer: A: Goseq plot
... Hi Al, Even though the spline is fit on all the data (green line) the plot is made by binning the genes according the length or number of reads and calculating the proportion of DE in each bin. Therefore you get fewer points than the number of DE genes. As you know to just plot genes individually i ...
written 5.7 years ago by Alicia Oshlack100
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Answer: A: Goseq plot
... Hi Al, To me the plot looks like a perfectly good fit to the data. The thing is that it doesn't look like there is much gene length bias in the plot that you have shown. I'm not really sure why this would be as it is usually a strong effect but perhaps the biological signal is even stronger than th ...
written 5.7 years ago by Alicia Oshlack100
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
... Hi Vanessa, In answer to your question number 2, in order for you to use a genome which is not supported (if it's not in UCSC then it's not supported in goseq) then you are right in that you will need the annotation (gene length) and the mapping from geneids to GO terms. It's not enough just to ha ...
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GOseq error
... Hi Iain, I'm not sure what this error is but how does the pwf look when you run nullp()? Does it look like a reasonable distribution? Are you using the Wallenius approximation? Might be worth trying with method="Sampling" and see if you get the same error. Cheers, Alicia On 11/02/12 10:00 PM, "b ...
go goseq written 5.8 years ago by Alicia Oshlack100 • updated 5.8 years ago by Iain Gallagher910
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goSeq error (steve Shen)
... Hi Steve, So it works OK if you use the more accurate "Sampling" method but not if you use the approximation. It's not clear to me why it's not working for the down category but does the pwf look ok when you generate it? Are there many genes DE for the down list? Cheers, Alicia > Message: 1 ...
go category edger goseq written 6.1 years ago by Alicia Oshlack100
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Answer: A: goseq - overrepresented p-values
... Hi Gu Mi, I think your interpretation of over-represented and under-represented is correct. Over-represented means that there are more DE genes in the category than we would expect given the size of the category and the gene length distribution so that would be enriched for DE genes. Under-represen ...
written 6.4 years ago by Alicia Oshlack100
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Answer: A: ChIP-Seq Normalization - Quantile (Rank) normalization
... Hi Henry, In my view it's not obvious how you would perform quantile normalization on ChIP-seq data. Were you planning to bin the data then quantile normalize binned counts? Then you run into the issue of what bin size to use for all you analysis and most peak-finding programs will not take binned ...
written 6.5 years ago by Alicia Oshlack100

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