Question: logFC , Limma (microArray Analysis)
0
gravatar for Cherif Ben Hamda
5.5 years ago by
Tunisia
Cherif Ben Hamda150 wrote:
Hello Hope that everything is good for you ! i have a strange results in my work ( series_matrix.txt microarray analysis ) and i don't know if it's normal or not ! i get high value (logFC) logFC AveExpr t P.Value adj.P.Val B 14990 *184.8393 *279.5879 7.053297 6.558774e-08 0.001457032 -3.553707 11016 *-113.2735* 132.3939 -6.777861 1.404067e-07 0.001559568 -3.588662 583 *565.7128 * 942.2667 -6.602527 2.288115e-07 0.001694349 -3.611925 21147 -*103.8393* 411.5121 -6.436832 3.639169e-07 0.002021103 -3.634652 2067 -*173.5342* 357.1273 -6.261612 5.958922e-07 0.002647549 -3.659485 5404 -*427.6940 * 464.8182 -6.131110 8.616234e-07 0.002968063 -3.678522 i show my method : gse <- getGEO(filename='GSE1849-GPL96_series_matrix.txt.gz') i make the design and after that i make analysis with limma : library(limma) fit <- lmFit(exprs(gse), design) contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , levels=design) contrast.matrix Ctrl_fits <- contrasts.fit(fit, contrast.matrix) Ctrl_ebFit <- eBayes(Ctrl_fits) nrow(topTable(Ctrl_ebFit, adjust = "BH", coef = 1, number = Inf) So it's normal or not ? i made mistake in my R code ? someone can help me ? Thank you so much Best, cherif [[alternative HTML version deleted]]
limma • 1.1k views
ADD COMMENTlink modified 5.5 years ago by James W. MacDonald51k • written 5.5 years ago by Cherif Ben Hamda150
Answer: logFC , Limma (microArray Analysis)
0
gravatar for James W. MacDonald
5.5 years ago by
United States
James W. MacDonald51k wrote:
Hi Cherif, It would be a good idea to look at the data first. I simply googled your GSE number and clicked on one of the samples, and it says this: *ID_REF* *VALUE* Signal intensity value, computed by MAS5. Scaled to 500 *ABS_CALL* Detection call *DETECTION P-VALUE* Detection P-value And if you look at your data you will notice that everything is strictly positive, and the maximum is somewhere near 1e14 or so. These are both indications that your data have not been logged, which is necessary for the analysis of these data. Best, Jim On 4/6/2014 12:48 PM, BEN HAMDA Cherif wrote: > Hello > Hope that everything is good for you ! > > i have a strange results in my work ( series_matrix.txt microarray > analysis ) > and i don't know if it's normal or not ! > > i get high value (logFC) > > logFC AveExpr t P.Value adj.P.Val > B > 14990 *184.8393 *279.5879 7.053297 6.558774e-08 0.001457032 -3.553707 > 11016 *-113.2735* 132.3939 -6.777861 1.404067e-07 0.001559568 -3.588662 > 583 *565.7128 * 942.2667 -6.602527 2.288115e-07 0.001694349 -3.611925 > 21147 -*103.8393* 411.5121 -6.436832 3.639169e-07 0.002021103 -3.634652 > 2067 -*173.5342* 357.1273 -6.261612 5.958922e-07 0.002647549 -3.659485 > 5404 -*427.6940 * 464.8182 -6.131110 8.616234e-07 0.002968063 -3.678522 > > i show my method : > > gse <- getGEO(filename='GSE1849-GPL96_series_matrix.txt.gz') > > i make the design and after that i make analysis with limma : > > library(limma) > fit <- lmFit(exprs(gse), design) > contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , levels=design) > contrast.matrix > Ctrl_fits <- contrasts.fit(fit, contrast.matrix) > Ctrl_ebFit <- eBayes(Ctrl_fits) > nrow(topTable(Ctrl_ebFit, adjust = "BH", coef = 1, number = Inf) > > So it's normal or not ? i made mistake in my R code ? someone can help me ? > > Thank you so much > > Best, > cherif > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.5 years ago by James W. MacDonald51k
Hi Jim, Thank you for your response. It's Ok right know. thanks a lot Best, Cherif 2014-04-07 15:01 GMT+01:00 James W. MacDonald <jmacdon@uw.edu>: > Hi Cherif, > > It would be a good idea to look at the data first. I simply googled your > GSE number and clicked on one of the samples, and it says this: > > *ID_REF* > *VALUE* Signal intensity value, computed by MAS5. Scaled to 500 > *ABS_CALL* Detection call > *DETECTION P-VALUE* Detection P-value > > > And if you look at your data you will notice that everything is strictly > positive, and the maximum is somewhere near 1e14 or so. These are both > indications that your data have not been logged, which is necessary for the > analysis of these data. > > Best, > > Jim > > > > On 4/6/2014 12:48 PM, BEN HAMDA Cherif wrote: > >> Hello >> Hope that everything is good for you ! >> >> i have a strange results in my work ( series_matrix.txt microarray >> analysis ) >> and i don't know if it's normal or not ! >> >> i get high value (logFC) >> >> logFC AveExpr t P.Value adj.P.Val >> B >> 14990 *184.8393 *279.5879 7.053297 6.558774e-08 0.001457032 -3.553707 >> 11016 *-113.2735* 132.3939 -6.777861 1.404067e-07 0.001559568 -3.588662 >> 583 *565.7128 * 942.2667 -6.602527 2.288115e-07 0.001694349 >> -3.611925 >> 21147 -*103.8393* 411.5121 -6.436832 3.639169e-07 0.002021103 -3.634652 >> 2067 -*173.5342* 357.1273 -6.261612 5.958922e-07 0.002647549 -3.659485 >> 5404 -*427.6940 * 464.8182 -6.131110 8.616234e-07 0.002968063 -3.678522 >> >> >> i show my method : >> >> gse <- getGEO(filename='GSE1849-GPL96_series_matrix.txt.gz') >> >> i make the design and after that i make analysis with limma : >> >> library(limma) >> fit <- lmFit(exprs(gse), design) >> contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , >> levels=design) >> contrast.matrix >> Ctrl_fits <- contrasts.fit(fit, contrast.matrix) >> Ctrl_ebFit <- eBayes(Ctrl_fits) >> nrow(topTable(Ctrl_ebFit, adjust = "BH", coef = 1, number = Inf) >> >> So it's normal or not ? i made mistake in my R code ? someone can help me >> ? >> >> Thank you so much >> >> Best, >> cherif >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.5 years ago by Cherif Ben Hamda150
Answer: logFC , Limma (microArray Analysis)
0
gravatar for Gordon Smyth
5.5 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
You have to log-transform the data. The data matrix contains unlogged intensities, but limma works with log2-intensities. The normalization may also be suspect. Gordon --------- original message ---------- [BioC] logFC , Limma (microArray Analysis) BEN HAMDA Cherif cherifbenhamda at gmail.com Sun Apr 6 18:48:20 CEST 2014 Hello Hope that everything is good for you ! i have a strange results in my work ( series_matrix.txt microarray analysis ) and i don't know if it's normal or not ! i get high value (logFC) logFC AveExpr t P.Value adj.P.Val B 14990 *184.8393 *279.5879 7.053297 6.558774e-08 0.001457032 -3.553707 11016 *-113.2735* 132.3939 -6.777861 1.404067e-07 0.001559568 -3.588662 583 *565.7128 * 942.2667 -6.602527 2.288115e-07 0.001694349 -3.611925 21147 -*103.8393* 411.5121 -6.436832 3.639169e-07 0.002021103 -3.634652 2067 -*173.5342* 357.1273 -6.261612 5.958922e-07 0.002647549 -3.659485 5404 -*427.6940 * 464.8182 -6.131110 8.616234e-07 0.002968063 -3.678522 i show my method : gse <- getGEO(filename='GSE1849-GPL96_series_matrix.txt.gz') i make the design and after that i make analysis with limma : library(limma) fit <- lmFit(exprs(gse), design) contrast.matrix <- makeContrasts(Normal_ACS = Normal - ACS , levels=design) contrast.matrix Ctrl_fits <- contrasts.fit(fit, contrast.matrix) Ctrl_ebFit <- eBayes(Ctrl_fits) nrow(topTable(Ctrl_ebFit, adjust = "BH", coef = 1, number = Inf) So it's normal or not ? i made mistake in my R code ? someone can help me? Thank you so much Best, cherif ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
ADD COMMENTlink written 5.5 years ago by Gordon Smyth38k
Hi Gordon, Thank you for your response. It's Ok right know Thank you very much Best, Cherif [[alternative HTML version deleted]]
ADD REPLYlink written 5.5 years ago by Cherif Ben Hamda150
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