User: Guillaume Robert

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Posts by Guillaume Robert

<prev • 15 results • page 1 of 2 • next >
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Comment: C: DESeq2 positive results for genes with high samples counts dispersion
... Ok thank you very much for this information, I will dig into lfcShrink ! ...
written 6 days ago by Guillaume Robert0
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DESeq2 positive results for genes with high samples counts dispersion
... Hi all, Sorry for this naive question, but I haven't been able to find a response anywhere. I'm using DESeq2 to find DE genes between two conditions on RNAseq public data, with 19 "non responders" samples, and 22 "responders" samples. After the DE analysis I've checked the samples read counts of ...
deseq2 written 6 days ago by Guillaume Robert0 • updated 6 days ago by Michael Love24k
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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 4 months ago by Guillaume Robert0
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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 4 months ago by Guillaume Robert0 • updated 4 months ago by Gordon Smyth37k
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Comment: C: Limma import array layout GenePix files
... It's working fine! Thank you again for your precious help. ...
written 4 months ago by Guillaume Robert0
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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 4 months ago by Guillaume Robert0 • updated 4 months ago by Gordon Smyth37k
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Comment: C: Limma filtering low expressed probes
... Ok thank you for the precision, I will skip probe filtering then. ...
written 4 months ago by Guillaume Robert0
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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 4 months ago by Guillaume Robert0 • updated 4 months ago by Gordon Smyth37k
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Comment: C: Limma import .gpr file error
... Ok I will keep the flagged lines then. Thanks for the informations. ...
written 4 months ago by Guillaume Robert0
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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 5 months ago by Guillaume Robert0

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