User: Guillaume Robert

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Posts by Guillaume Robert

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Limma design matrix separate channel analysis with same control
... Thank you for your response. It works fine this way ! ...
written 11 weeks ago by Guillaume Robert • 0
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Limma design matrix separate channel analysis with same control
... Hi all, I'm currently analysing a microarray dataset, on which I'm trying to detect the difference of gene expression between responders and non responders to a treatment. Even after reading the Limma user guide and searching on the forum I'm not really sure which design matrix I should use for th ...
limma design matrix gene expression written 12 weeks ago by Guillaume Robert • 0 • updated 12 weeks ago by Gordon Smyth ♦ 37k
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Comment: C: Limma import array layout GenePix files
... It's working fine! Thank you again for your precious help. ...
written 3 months ago by Guillaume Robert • 0
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Limma import array layout GenePix files
... Hi everyone, I'm currently analyzing a public microarray dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/) I've managed to import the GenePix files into limma thank to the commands : cols = list(R = "GenePix:F635 Mean", G = "GenePix:F532 Mean", Rb = "GenePix:B635 Medi ...
microarray limma layout written 3 months ago by Guillaume Robert • 0 • updated 3 months ago by Gordon Smyth ♦ 37k
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Comment: C: Limma filtering low expressed probes
... Ok thank you for the precision, I will skip probe filtering then. ...
written 3 months ago by Guillaume Robert • 0
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Limma filtering low expressed probes
... Hi all, All my apologies for this trivial question, but I haven't been able to find a solution anywhere. I've got a MAlist object encompassing the expression data of 62 arrays. In the chapter 7 of the limma user guide it is advised to filter for probes that are not expressed, by keeping only prob ...
microarray limma written 3 months ago by Guillaume Robert • 0 • updated 3 months ago by Gordon Smyth ♦ 37k
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Comment: C: Limma import .gpr file error
... Ok I will keep the flagged lines then. Thanks for the informations. ...
written 3 months ago by Guillaume Robert • 0
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Comment: C: Limma import .gpr file error
... Thank you for your response. Why would you skipped the flag filtering? I've looked into the file and found several probes flagged with either -100, -75 or -50, but I haven't found the meaning of those flags. ...
written 3 months ago by Guillaume Robert • 0
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Comment: C: Limma import .gpr file error
... Ok thank you very much it's working now. ...
written 3 months ago by Guillaume Robert • 0
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Limma import .gpr file error
... Hi all, Sorry for this maybe naive question, but I never analysed microarray before. I'm trying to import .gpr files from a public dataset (https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-104/) in limma thanks to the function read.maimages(). As specified in the documentation I've created a ...
microarray limma gpr written 3 months ago by Guillaume Robert • 0 • updated 3 months ago by Gordon Smyth ♦ 37k

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