User: alessandro.guffanti@genomnia.com

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Posts by alessandro.guffanti@genomnia.com

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Comment: C: extracting CPM from a DGElist after normalization in edgeR
... Hello - thanks also for this second clarification. I actually read this help line, but it was a bit obscure to me Let me try to summarize: > colSums*(**cpm(currentDiff$counts)*) , where currentDiff is a DGEList object after normalization LT1C LT2C LT3C ST2C ST4C ST10C ST12C ST5C ST7C S ...
written 5.7 years ago by alessandro.guffanti@genomnia.com330
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Comment: C: extracting CPM from a DGElist after normalization in edgeR
... Thanks for the kind answer, Alessandro & colleagues Il 03/04/2014 14:51, Devon Ryan ha scritto: > The difference in output when running cpm() on a matrix and a DGEList > is due to the latter using the normalized library size. In other > words, the latter method does: > > t(t(cur ...
written 5.7 years ago by alessandro.guffanti@genomnia.com330
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extracting CPM from a DGElist after normalization in edgeR
... Dear colleagues and dear Mark: We want to extract the CPM from a DGElist object after TMM normalization, common and tagwise dispersion evaluation. Here is a sample of the code, it's just a standard edgeR DEG workflow: samplesheet1 <- read.delim("sample_sheet.txt", stringsAsFactors = FALSE) com ...
edger written 5.7 years ago by alessandro.guffanti@genomnia.com330 • updated 5.7 years ago by Gordon Smyth39k
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Comment: C: edgeR on ncRNA analysis question
... I will check wether this was the case ! Thanks again Alessandro ----------------------------------------------------- Alessandro Guffanti - Head, Bioinformatics Genomnia srl Via Nerviano, 31/B – 20020 Lainate (MI) Tel. +39-0293305.702 / Fax +39-0293305.777 www.genomnia.com [http://www.genomnia.c ...
written 6.0 years ago by alessandro.guffanti@genomnia.com330
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Answer: A: edgeR on ncRNA analysis question
... Hi - OK, thanks for the feedback, I will them look carefully at the procedure No, I did not have only WTA, but in the two comparisons the experiment samples were different - i.e. these are the same W.T. samples compared with two different set of experiment samples, which I did not copy in the outpu ...
written 6.0 years ago by alessandro.guffanti@genomnia.com330
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edgeR on ncRNA analysis question
... Der BioC edgeR developers and users: I am using edgeR for ncRNA transcriptome data analysis - ie mapping RNA seq results only versus a ncRNA transcript database (bowtie from Color Space reads) There seems to be, unsurprisingly, an high variability on these samples, which affects obviously the FDR ...
normalization edger written 6.0 years ago by alessandro.guffanti@genomnia.com330
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Comment: C: HTqPCR normalization issues - third posting
... Perfect thanks - indeed we don't have so many genes but we could give a try also at the lmFit() function Many thanks again, Alessandro On 11/12/2013 7:40 PM, Levi Waldron wrote: > A t-test on the delta-delta-Ct values is reasonable. However if you > have many more genes than samples, you m ...
written 6.1 years ago by alessandro.guffanti@genomnia.com330
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Comment: C: HTqPCR normalization issues - third posting
... Thanks a lot Levi! this is enlightening and we will use your function on our datasets, we will let you know how this goes. Just a final question, excuse me the sheer ignorance: if I want to associate a statistics to each final value (which is indeed the big added vakue of HTqPCR), of course in the ...
written 6.1 years ago by alessandro.guffanti@genomnia.com330
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HTqPCR normalization issues - third posting
... Dear Heidi good morning ! We made some more work on HTqPCR (actually, mainly Elena..) and we have an update and a question for you: => update: seemingly with the latest HTqPCR it is not possible to import anymore datasets in a simple format, gene name, Ct, group for example, with readCtData(). ...
normalization htqpcr written 6.1 years ago by alessandro.guffanti@genomnia.com330 • updated 6.1 years ago by Levi Waldron980
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Comment: C: HTqPCR normalization issues - third posting
... Thanks Heidi - maybe you have already seen what we describe, and hence there is an easy explanation which does not require further work on your side ? best wishes, Alessandro Hi Alessandro, > > my apologies for the lack of a response. I've recently had to take a > hiatus from Bioconducto ...
written 6.2 years ago by alessandro.guffanti@genomnia.com330

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