User: Guillaume Meurice

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Posts by Guillaume Meurice

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Comment: C: LIMMA : trying to take contrast of non estimable coefficient
... Dear James, thanks for your quick answer ! > Your design matrix is not full rank. In other words, at least one column is a linear combination of other columns. This is why it is usually best to use functionality to create the design matrix, rather than trying to create one by yourself. I'm try ...
written 7.2 years ago by Guillaume Meurice210
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LIMMA : trying to take contrast of non estimable coefficient
... Dear list, I'm using Agilent 44K microarray. We have 20 cases study. For each one we hybridized sample before and after treatment on the same array, in dye-swap. I have the following design matrix (build manually, to follow the group-mean parametrization approach) : === Intercept liver other R ...
microarray written 7.2 years ago by Guillaume Meurice210 • updated 7.2 years ago by James W. MacDonald49k
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Comment: C: Limma Dual Color Agilent : Mixed model or not?
... > Dear Guillaume, > > My apologies, I seem to have misread your experimental design. Reading your reply and looking more closely at your targets frame, I now see that your design is a two-group problem with replicate- specific controls and technical dye-swaps. Right? You're totally right. ...
written 7.3 years ago by Guillaume Meurice210
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Limma Dual Color Agilent : Mixed model or not ?
... Dear all, I have the project with the following design (dual color, with dye swap): Cy5 Cy3 Status RepNum Polarity R1 SI31_vs_R1 CTRL+ R1_SI31 R1_CTRL R 1 + R1 SI31_vs_R1 CTRL- R1_CTRL R1_SI31 R 1 - R2 SI31_vs_R2 CTRL+ R2_SI31 R2_CTRL ...
written 7.3 years ago by Guillaume Meurice210
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Answer: A: 2 way anova in Bioconductor
... Dear All, I have a few more question regarding the design matrix bellow (mainly How to interpret the coefficient ?) > > design > (Intercept) Sex1 Time1 Time2 Sex1:Time1 Sex1:Time2 > 1 1 -1 -1 -1 1 1 > 2 1 -1 0 1 0 ...
written 7.7 years ago by Guillaume Meurice210
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Comment: C: arrayQualityMEtrics
... Dear Wolfgang, many thanks for your answer, and you were right : loading Biobase solved the problem. Best regards -- Guillaume > Dear Guillaume > > Can you try again after: > library("Biobase") > > What seems to happen is the following: arrayQualityMetrics wants to convert your ...
written 7.8 years ago by Guillaume Meurice210
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arrayQualityMEtrics
... Dear All, I encounter the following probleme with arrayQualityMetrics (v3.8.0) : > arrayQualityMetrics(RG, outdir="aqmRaw", do.logtransform=T) The report will be written into directory 'aqmRaw'. Error in eval(expr, envir, enclos) : could not find function "note" Error in prepdata(expressionset, ...
convert arrayqualitymetrics written 7.8 years ago by Guillaume Meurice210 • updated 7.8 years ago by Wolfgang Huber13k
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Answer: A: limma analysis of 2-color experiment with tech reps [was: Help with]
... Dear Gordon, many thanks for your answer. > I am going to assume that the main purpose of your experiment is to find genes for which the d7 vs d1 response is different between the two groups of patients. you're right, this exactly what I'm looking for. > > Since you have gone to the tr ...
written 7.8 years ago by Guillaume Meurice210
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Answer: A: Help with
... Sorry, I made some mistake in my previous mail, into the contrast matrix (bad copy paste from another project), so here I have corrected them. > I have a question regarding the way to properly design biological replicate and technical replicates. > > In the projet, we have two groups of sa ...
written 7.8 years ago by Guillaume Meurice210
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Help with
... Dear all, I have a question regarding the way to properly design biological replicate and technical replicates. In the projet, we have two groups of sample : R (respond to the treatment), NR (no response). For each groups, there is several replicates (3) that come from different patients (so not ...
written 7.8 years ago by Guillaume Meurice210

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