User: Heidi Dvinge

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Heidi Dvinge2.0k
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Posts by Heidi Dvinge

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Comment: C: HTqPCR normalization issues - third posting
... On 10/10/2013 09:35, heidi wrote: > On 10/10/2013 07:40, alessandro.guffanti at genomnia.com wrote: >> Thanks, much appreciated ! >> It would be important for us to understand wether we are doing >> something fundamental wrong, or if there actually is a bug on the >> softw ...
written 4.1 years ago by Heidi Dvinge2.0k
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Comment: C: HTqPCR normalization issues - third posting
... On 10/10/2013 07:40, alessandro.guffanti at genomnia.com wrote: > Thanks, much appreciated ! > > It would be important for us to understand wether we are doing > something fundamental wrong, or if there actually is a bug on the > software (happens), because we are using heavily this ...
written 4.1 years ago by Heidi Dvinge2.0k
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HTqPCR error
... > Dear Heidi, > > After trying the two combinations that you talked about, just the second > one worked, i.e: > > raw1 <- readCtData(files="Prueba_Blanco001.txt", n.features=96, n.data=96, > column.info=list(flag=9, feature=5, type=6, Ct=7, position=1), skip=12, > sep="\t" ...
htqpcr written 5.2 years ago by Heidi Dvinge2.0k
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HTqPCR Release 2.10
... Hi Victoria, > Dear Heidi, > > Do you still maintain the Bioconductor HTqPCR Release 2.10? > HTqPCR is currently at version 1.11.2, so I assume you mean the version corresponding to R 2.10. It's not maintained as such, but it's still available at http://www.bioconductor.org/packages/2.1 ...
htqpcr written 5.2 years ago by Heidi Dvinge2.0k
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[Fwd: Re: HTqPCR error]
... Hi Juan, > Dear Heidi, > > My name is Juan Fernandez-Tajes and I?m using HTqPCR for analyzing some > Biomark 96*96 data. When I tried the following command I got an error: > >>raw1 <- readCtData(files="Prueba_Blanco001.txt", format="BioMark", >> n.features=96, n.data=9 ...
htqpcr written 5.2 years ago by Heidi Dvinge2.0k
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HTqPCR
... Hi Mala, > Hi Heidi, > > We have some question regarding the ddCt and Fold change value > calculation in HTqPCR. On creating contrasts, if we have Mt-Wt (Mt=mutant, > Wt= WildType), does the +ve fold change suggest that it is higher in the > Mutant or Wild Type. I assume you're ...
qpcr limma ddct htqpcr written 5.2 years ago by Heidi Dvinge2.0k
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Answer: A: HTqPCR: number of samples, number of features
... Hi Alex, > hi, > I've been given an SDS raw file (see below) which contains embedded 10 > cards of 348 wells each. > The genes are totally 48 and each card has 4 samples so totally 40 > samples. > If I am correct n.features should be = 3480 and the n.data (the number of > sampl ...
written 5.2 years ago by Heidi Dvinge2.0k
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Answer: A: Fwd: help
... Hello Rakesh, > mam, >> qDE.ttest <- ttestCtData(sr.norm[, 1:5], groups = files$Treatment[1:5], > calibrator = "Control") > > it works well but it give ddct without entering referance gene name > I'm not sure I understand your question. There isn't a one single reference gen ...
written 5.3 years ago by Heidi Dvinge2.0k
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Answer: A: Fwd: help
... Hello Rakesh, > > sir, > i am new on R language and dealing with light-cycler qpcr data using > HtqPCR package.everything goes all right till fold change. > > when i use t-test then following error occured. > >> qDE.ttest <- ttestCtData(sr.norm[, 1:2], groups = file ...
written 5.3 years ago by Heidi Dvinge2.0k
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Comment: C: Openening qPCR file from ABI
... Hi Philippe, Guido This is indeed the case. E.g. library(HTqPCR) raw.data <- readCtData(files=..., format="SDS") That will give you an object of class qPCRset. From then on you can directly continue using HTqPCR for normalisation, visualisation and testing. Or, if you already have some other w ...
written 5.3 years ago by Heidi Dvinge2.0k

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