User: Massimo Pinto

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Massimo Pinto390
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Posts by Massimo Pinto

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Comment: C: Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... Dear Francois, Tobias, and all users Thanks to this discussion, and those that I have found on the Archives, as Francois suggested, I am more aware now of the importance of avoiding averages of different probes that map the same gene transcript at different locations.?I should now perhaps test - on ...
written 10.1 years ago by Massimo Pinto390
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Comment: C: Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... I must confess I had completely forgotten the issue of RNA splicing. Shame on me. Thank you very much for the key info that you provided and for the conversation that you embarked on. I am going back to this immediately. Yours, Massimo On Wed, Oct 21, 2009 at 4:48 PM, Francois Pepin wrote: > T ...
written 10.1 years ago by Massimo Pinto390
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Comment: C: an apparently strange case of 'Warning: number of items to replace is not a mult
... That was indeed the case. Thank you, James. This has revealed a problem that refers, possibly, to pre-processing and which is now subject of a dedicated thread: https://stat.ethz.ch/pipermail/bioconductor/2009-October/030100.html Yours Massimo Massimo Pinto Post Doctoral Research Fellow Enrico Ferm ...
written 10.1 years ago by Massimo Pinto390
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Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets
... Greetings all, I realised that I was carrying forward, in my analysis, multiple measurements for the same gene that had been carried out using independent probes. This is a feature of Agilent arrays, as I understand. However, while it is clear to me that Agi4x44PreProcess offers a function to summa ...
hgug4112a written 10.1 years ago by Massimo Pinto390 • updated 10.1 years ago by Francois Pepin1.3k
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an apparently strange case of 'Warning: number of items to replace is not a multiple of replacement length'
... Greetings, I have encountered a series of warning messages when copying indices into a vector of integers. Specifically: > Geni_GO_0033554_CM3.ctr3 <- as.integer(unlist(geneIdsByCategory(hgOver.6, "GO:0033554"), use.names = FALSE)) [1] 100133315 10714 1112 11198 1643 ...
go hgug4112a written 10.1 years ago by Massimo Pinto390 • updated 10.1 years ago by James W. MacDonald51k
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From a list of annotated interesting genes to a list of GO's 'interesting' Biological Processes
... Greetings all, Using limma's fitting approach and topTable(), I have reached the nice point of having produced lists of annotated interesting genes. Graphically, I can now compare across my contrasts using Venn diagrams, and I can build Volcano plots etc. As I am making my early steps into Gene O ...
gostats written 10.3 years ago by Massimo Pinto390
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Comment: C: Two interaction coefficients not estimable in limma's lmFit() in a 2^3 factorial
... James and all, I thought of reporting here a few final remarks on this issue, in case anyone will be every taking advantage from this thread. Here I was trying to estimate 8 parameters when I only had 6 data points (with four replicates each). At maximum, I could estimate just 6 parameters. In my ...
written 10.3 years ago by Massimo Pinto390
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Comment: C: Two interaction coefficients not estimable in limma's lmFit() in a 2^3 factorial
... thank you Jim, you are indeed correct: I did not specify how I created my matrix. Here it comes ==== Dose <- factor(targets$Dose, levels=c("Cn", "1Gy")) # It's very important that you define the levels now, with their order, as otherwise he will do it for you and this may not be the way you wan ...
written 10.3 years ago by Massimo Pinto390
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Two interaction coefficients not estimable in limma's lmFit() in a 2^3 factorial design - does this change my contrast matrix now?
... Greetings all, I have noticed that several users have presented the issue of parameters not estimated in some cases of linear model fittings with the limma function lmFit(). In trying to implement my 2^3 factorial design, I have followed Bioinformatics and Computational Biology Solutions using R a ...
limma written 10.3 years ago by Massimo Pinto390 • updated 10.3 years ago by James W. MacDonald51k
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Agi4x44PreProcess probe summarization bug?
... Hi Tobias, I am trying to figure out what would be the effect of this potential bug. Have you tried to correct the function to see what happens when MED is returned? Massimo -- Massimo Pinto Post Doctoral Research Fellow Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome h ...
written 10.3 years ago by Massimo Pinto390 • updated 10.3 years ago by Tobias Straub410

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