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Question: [limma] [Rfit] [samr] Gene expression distribution using lmFit and eBayes
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gravatar for Jérôme Lane
5.0 years ago by
Jérôme Lane30 wrote:
Hi, The 3/4 of my microarray gene expressions have non normal distribution with most of p-values after Shapiro test under 10x-5. I tried linear ranked regression from rfit (no normality assumption for residues) from Rfit package for adjustment of covariables + SAM (non parametric) from samr package but results where not as biologically relevant as lmFit + eBayes could provide. I know that lmFit function can analyses gene expression not strictly normal, but what is the limit ? Is it statistically relevant to use lmFit + eBayes according to my data ? Best regards, J??r??me Lane
ADD COMMENTlink modified 5.0 years ago by Gordon Smyth35k • written 5.0 years ago by Jérôme Lane30
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gravatar for Gordon Smyth
5.0 years ago by
Gordon Smyth35k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth35k wrote:
Dear Jerome, The Shapiro test is only applicable to iid samples, so it is difficult to see how it could be used to test normality of expression values in a linear modelling context. If you have applied the test to the normalized expression values for each gene, then I suspect that the test is actually picking up differential expression rather than non-normality. The limma code is very robust against non-normality. All the usual microarray platforms and standard preprocessing procedures produce data that is normally distributed to a good enough approximation. Much effort has been devoted to developing good preprocessing and normalization algorithms. The concept of "robustness" in statistical analysis goes back a 1953 paper by George Box in Biometrika. In that paper, Box wrote of the "remarkable property of robustness to non-normality which [tests for comparing means] possess". The tests done by limma inherit the robustness property that Box was referring to. Box made the point that the robustness of the two sample t-test was not improved by checking first for equal variances. He said "To make the preliminary test on variances is rather like putting to sea in a rowing boat to find out whether conditions are sufficiently calm for an ocean liner to leave port!" I rather think that, if Box was still alive today, he might say something similar about a preliminary Shapiro test! Best wishes Gordon > Date: Thu, 21 Nov 2013 17:42:21 -0500 > From: Jerome Lane <jerome.lane at="" criucpq.ulaval.ca=""> > To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] [limma] [Rfit] [samr] Gene expression distribution > using lmFit and eBayes > > Hi, > > The 3/4 of my microarray gene expressions have non normal distribution with > most of p-values after Shapiro test under 10x-5. > > I tried linear ranked regression from rfit (no normality assumption for > residues) from Rfit package for adjustment of covariables + SAM (non > parametric) from samr package but results where not as biologically relevant > as lmFit + eBayes could provide. > > I know that lmFit function can analyses gene expression not strictly normal, > but what is the limit ? > > Is it statistically relevant to use lmFit + eBayes according to my data ? > > Best regards, > > Jerome Lane ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 5.0 years ago by Gordon Smyth35k
Dear Gordon, Thanks for the reply, I appreciated it very much. Is there a way to determine the ? quality ? of normalization for genes ? Best regards, Jerome Le 2013-11-22 20:55, ? Gordon K Smyth ? <smyth at="" wehi.edu.au=""> a ?crit : >Dear Jerome, > >The Shapiro test is only applicable to iid samples, so it is difficult to >see how it could be used to test normality of expression values in a >linear modelling context. If you have applied the test to the normalized >expression values for each gene, then I suspect that the test is actually >picking up differential expression rather than non-normality. > >The limma code is very robust against non-normality. All the usual >microarray platforms and standard preprocessing procedures produce data >that is normally distributed to a good enough approximation. Much effort >has been devoted to developing good preprocessing and normalization >algorithms. > >The concept of "robustness" in statistical analysis goes back a 1953 >paper >by George Box in Biometrika. In that paper, Box wrote of the "remarkable >property of robustness to non-normality which [tests for comparing means] >possess". The tests done by limma inherit the robustness property that >Box was referring to. Box made the point that the robustness of the two >sample t-test was not improved by checking first for equal variances. He >said > >"To make the preliminary test on variances is rather like putting to sea >in a rowing boat to find out whether conditions are sufficiently calm for >an ocean liner to leave port!" > >I rather think that, if Box was still alive today, he might say something >similar about a preliminary Shapiro test! > >Best wishes >Gordon > >> Date: Thu, 21 Nov 2013 17:42:21 -0500 >> From: Jerome Lane <jerome.lane at="" criucpq.ulaval.ca=""> >> To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> >> Subject: [BioC] [limma] [Rfit] [samr] Gene expression distribution >> using lmFit and eBayes >> >> Hi, >> >> The 3/4 of my microarray gene expressions have non normal >>distribution with >> most of p-values after Shapiro test under 10x-5. >> >> I tried linear ranked regression from rfit (no normality assumption >>for >> residues) from Rfit package for adjustment of covariables + SAM (non >> parametric) from samr package but results where not as biologically >>relevant >> as lmFit + eBayes could provide. >> >> I know that lmFit function can analyses gene expression not strictly >>normal, >> but what is the limit ? >> >> Is it statistically relevant to use lmFit + eBayes according to my >>data ? >> >> Best regards, >> >> Jerome Lane > >_____________________________________________________________________ _ >The information in this email is confidential and inten...{{dropped:6}}
ADD REPLYlink written 5.0 years ago by Jérôme Lane30
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