User: Giulio Di Giovanni

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Posts by Giulio Di Giovanni

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Answer: A: Limma design for single channel arrays with technical repeats
... Hi all, I work with one-channel arrays, where on each slide the sample is repeated three times (in three blocks called subarrays). In order to perform the differential expression analysis (usually a two-groups comparison), up to now we always averaged the three repetitions (after normali ...
written 6.3 years ago by Giulio Di Giovanni540
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... http://www.zirconia-wedding-ring.14niche.info/wp- content/themes/classic/mylife.html [[alternative HTML version deleted]] ...
written 8.5 years ago by Giulio Di Giovanni540
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Comment: C: Normalization quality assessment tools?
... Dear Wolfgang, thanks a lot for your help and suggestions. You're right, I didn't explained it very well skipping details of what I "want to normalize". Accordingly to Nathman et al. (1997) we identified many sources of technical variation through the use of linear mixed models, and we removed them ...
written 8.7 years ago by Giulio Di Giovanni540
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Normalization quality assessment tools?
... Hi all, I've an experiment with almost 300 arrays, single channel (not Affymetrix, but some in-house made peptide arrays). Differently from all my past experiments, this time I have the suspicion that the normalization step it's not necessary, or worse.1) the qqplot of unnormalized intensities se ...
normalization convert written 8.7 years ago by Giulio Di Giovanni540 • updated 8.7 years ago by Wolfgang Huber13k
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Annotate getSEQ weird behaviour.
... Maybe it's only a temporary thing, but if I follow the help > library(annotate) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation ...
written 8.8 years ago by Giulio Di Giovanni540 • updated 8.8 years ago by Martin Morgan ♦♦ 23k
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Right skewed histogram of p-values
... Hi. During a DE analysis, done with limma ebayes and toptable, the histogram of the p-values doesn't show a high number of low p-values, and not even an uniform distribution, which I may expect under the null hypothesis of no-differentiation (right?), but something totally skewed to the right: low ...
limma written 9.1 years ago by Giulio Di Giovanni540 • updated 9.1 years ago by Simon Anders3.6k
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Answer: A: Puzzled about limma and PAM results validity
... Mhhh, it seems that maybe I wasn't clear, or my previous it passed unnoticed. Please allow me to repost it (see below this email). In short: Quite clearly small differentiate genes with Differential Expression. Same results, same genes with PAM, but high CV errors! Is it PAM """failing""", by overe ...
written 9.1 years ago by Giulio Di Giovanni540
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Puzzled about limma and PAM results validity
... Hi all, sorry if I write such a "not strictly technical" question to this mailing list. Even if not linked to the programming, maybe somebody would be so nice to comment on my issue. On a dataset I performed a simple DE analysis between two groups through limma (eBayes and topTable). The histogra ...
limma written 9.1 years ago by Giulio Di Giovanni540
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Protein Codes to Protein Names
... Hi all, I'm working with proteins. Does anybody knows which is the easiest way and the appropriate package to retrieve some protein names starting from proteins codes? Example: Q7VYR0 -> GTP-binding elongation factor CAA09473 -> P.69A protein (pertactin) AAA22974 -> filame ...
written 9.6 years ago by Giulio Di Giovanni540 • updated 9.6 years ago by Cristobal Fresno Rodríguez360
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Answer: A: rtracklayer browserView
... Ok, found it, thanks anyway. while laying the track using (layTrack) it is possible to set graphType="points" to display points instead than bars and also autoScale=F and viewLimits=c(minY,maxY) to set the data range Y limits. Thanks D > From: perimessaggini@hotmail.com > To: bioconduc ...
written 10.1 years ago by Giulio Di Giovanni540

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Popular Question 6.3 years ago, created a question with more than 1,000 views. For Right skewed histogram of p-values

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