User: Matthew Hannah

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Posts by Matthew Hannah

<prev • 94 results • page 2 of 10 • next >
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Answer: A: Cy3 Cy5 mixup?
... Dennis, I noticed this on a 'excursion' back to the lab, at first glance confusing. Cy3 DYE is red and Cy5 DYE is blue, they often also have packaging in these colours. However, the adsorption maxima are 532 and 649, and the florescence maxima are 570 and 670 respectively. Therefore, Cy3 is detecte ...
written 14.1 years ago by Matthew Hannah940
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limma regression / fdr permutation correction
... Easter greetings, and a question ;-) I have 8 genotypes with 3 biological replicas per genotype. I also have a quantified variable (growth) for each. Currently I use a model like x <- c(1.5,1.5,1.5,2.3,2.3,2.3,3.6,3.6,3.6,4.2,4.2,4.2,4.8,4.8,4.8,5.2,5.2, 5. 2,5.5,5.5,5.5,6,6,6) design <- mode ...
written 14.1 years ago by Matthew Hannah940
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Answer: A: p-value adjustment
... One thing to add on this point that might be of interest is that an initial look at p.adjust p.adjust(p, method = p.adjust.methods, n = length(p)) would suggest that including NAs would result in more conservative correction as n > # of p-values, but it doesn't (at least for fdr) as the NAs are o ...
written 14.1 years ago by Matthew Hannah940
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Answer: A: Order in which ReadAffy() and read.affybatch()
... Hrishi, The bioC documentation, "introduction to R", short courses, BioC archive search and normal google reward the persistent. Here's a couple of pointers that may also help. #r ignores anything on the same line following a # help.start() # starts html help #?any command - opens the documentatio ...
written 14.1 years ago by Matthew Hannah940
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Answer: A: GCRMA: low intensity exprs estimates / pval distributions
... Hi, Just looking for opinions again. Basically any comments on the bimodal p-value distributions that can sometimes be observed when limma (although I guess this would apply for any test) is used to test for differential expression of data using the gcrma expression estimate. In my last mail I did ...
written 14.1 years ago by Matthew Hannah940
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GCRMA: low intensity exprs estimates / pval distributions
... Hi, I noticed this a while ago but with some of the recent threads, maybe now is suitable for a general discussion. This will be easiest if you view the attached files on the bioconductor archive site. Basically GCRMA changed it's BG parameter estimation from using a low quantile of strata of aff ...
gcrma written 14.1 years ago by Matthew Hannah940
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RMA verse GCRMA, low intensity
... Fangxin, You might want to experiment with eset <- justGCRMA(fast=F) as the fast version sets signals (or BGs?) that are close to BG to a constant value (search the lists for a better (correct) definition) which may give some bias for low signal values. However, you will still have differences i ...
cycle written 14.1 years ago by Matthew Hannah940
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Answer: A: kyte and doolittle hydropathy values/plot - sub + sliding window mean
... Hi, I've found one mistake, I didn't realise that strsplit returns a list within a list, so unlist(x) allows me to crudely call the score.assign function below. But it must be possible to replace them efficiently all at once? I wondered about the names function but don't see how to assign the valu ...
written 14.4 years ago by Matthew Hannah940
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kyte and doolittle hydropathy values/plot - sub + sliding window mean
... Hi, This algorithm calculates the hydropathy of proteins. I've found web-based versions but they all return a graph not values. I was wondering if there was an R/BioC inplementation of it, or something similar. Alternatively I'm trying to do something similar myself but have got stuck with no obvi ...
graph convert written 14.4 years ago by Matthew Hannah940
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limma p.values, tech replication and dup cor
... Hi, I've got a question about df.prior, df.residual and p.value from eBayes. df.prior seems to be number of arrays minus no of coefficients. ebayes$p.value is on (df.prior + df.residual). This leads to a strange? situation when I compare between a technically replicated (single channel) spotted oli ...
affy limma oligo written 14.5 years ago by Matthew Hannah940

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Popular Question 13.3 years ago, created a question with more than 1,000 views. For Selecting p-value cutoffs for differential expression

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