User: michael watson IAH-C

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Posts by michael watson IAH-C

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Comment: C: biomaRt connection problems
... Thanks Jim, Sean That URL just worked for me, so I guess there are intermittent problems Thanks Mick From: seandavi@gmail.com [mailto:seandavi@gmail.com] On Behalf Of Sean Davis Sent: 22 June 2010 13:57 To: michael watson (IAH-C) Cc: bioc list Subject: Re: [BioC] biomaRt connection problems On ...
written 7.4 years ago by michael watson IAH-C3.4k
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biomaRt connection problems
... Hi I've been having biomaRt connection problems all morning: > library(biomaRt) > mart <- useMart("ensembl", "btaurus_gene_ensembl") Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web serv ...
biomart written 7.4 years ago by michael watson IAH-C3.4k • updated 7.4 years ago by Sean Davis21k
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Comment: C: different color for a subset of points on heatmap
... I wouldn't necessarily change the colours (which mean something, scientifically). Not sure if anyone has mentioned it yet, but how about: library(gplots) library(geneplotter) mat <- matrix(rnorm(5000), ncol=10) heatmap.2(mat, key=FALSE, trace="none", col=greenred.colors(70), rowsep=c(50,100), s ...
written 7.4 years ago by michael watson IAH-C3.4k
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Answer: A: question about limma
... Hi Katie Can you post the code you used in limma, and specifically, the design and contrast (if there was one) matrices Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Taylor, Katie [kt70@leicester.ac ...
written 7.4 years ago by michael watson IAH-C3.4k
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Comment: C: DESeq and number of replicates required for RNA-Seq
... I guess the issue I am trying to highlight is one that Naomi put into a very good statistical framework – with ZERO biological variability, one would still need 8 replicates per treatment to detect a significant two-fold difference. Isn’t that slightly worrisome? Don’t get me wrong, I love th ...
written 7.4 years ago by michael watson IAH-C3.4k
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Comment: C: DESeq and number of replicates required for RNA-Seq
... Hi Cei These are not my datasets, and I have heard something similar to you. The history of this discussion is that I asked why DESeq, in the example data anaylsis, only found as significant genes whose fold change was very large (2^5 on average). I thought this was odd as low fold changes can be ...
written 7.4 years ago by michael watson IAH-C3.4k
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Comment: C: DESeq and number of replicates required for RNA-Seq
... Hi Mark Thanks for the reply. I drafted and sent en e-mail on my phone which then lost connectivity (and the message) so apologies if anyone gets something similar twice! What worries me here is that we are looking at gene expression; we have been for years, using technologies such as RT-PCR, mic ...
written 7.4 years ago by michael watson IAH-C3.4k
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Answer: A: Using Gostats on a new organism
... Hi This may not help you with GOstats, but we have example code on our website on how to use topGO: http://bioinformatics.iah.ac.uk/sample-code Thanks Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of ...
written 7.4 years ago by michael watson IAH-C3.4k
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Comment: C: DESeq and number of replicates required for RNA-Seq
... Thanks Naomi Yes, I have several RNA-Seq datasets that look like they may have large biological variation. I feel this is the "dirty secret" of the new revolution that is RNA- Seq - even with large numbers of replicates, the variation in (and nature of) the read counts means we can only find genes ...
written 7.4 years ago by michael watson IAH-C3.4k
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Comment: C: is there a 1:1 correspondence between ENST and 3'UTR sequence ?
... Hi Maura Of the three IDs you list, only ensembl_transcript_id is a unique identifier for transcripts. Not all transcripts have an annotated 3' UTR Mick ________________________________________ From: bioconductor-bounces@stat.math.ethz.ch [bioconductor- bounces@stat.math.ethz.ch] On Behalf Of Ste ...
written 7.4 years ago by michael watson IAH-C3.4k

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Popular Question 7.4 years ago, created a question with more than 1,000 views. For biomaRt connection problems
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