upregulated or downregulated?
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@biosciencegeekgmailcom-3471
Last seen 7.1 years ago
Hi, I have searched the mailing list but have found no solution.I have a set of 19 genes from two cancer types from a single dye experiment that have been analysed by limma. How do I know by looking at the logFC values which genes have been upregulated and downregulated? *Gene logFC adjusted p value* 1 4.503176282 8.16484E-07 2 3.098042379 0.001186095 3 2.478184614 6.25887E-06 4 2.123900966 0.000345836 5 2.072218463 0.000307254 6 1.861216801 0.019495491 7 1.60330851 0.000170216 8 1.371819046 0.041850715 9 1.32421397 0.002931049 10 1.290754778 1.6091E-05 11 1.110357905 0.011299876 12 -0.638346118 0.046342014 13 -0.661346419 0.019450208 14 -0.67761362 0.046342014 15 -0.90175871 0.020400911 16 -0.904514183 0.014558953 17 -1.015572133 0.046342014 18 -1.545921472 5.24644E-05 19 -3.499508887 1.58919E-06 [[alternative HTML version deleted]]
Cancer limma Cancer limma • 4.5k views
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@saroj-k-mohapatra-3419
Last seen 7.1 years ago
Hi, In the log-scale , positive value suggests up-regulation; negative down-regulation. For example: 2-fold up-regulation gives logFC of 1, 2-fold down-regulation (i.e., 0.5) gives -1. > log2(2) [1] 1 > log2(0.5) [1] -1 In the example you provided, genes 1-11 are up-regulated; the rest down. This assumes that the design and contrast matrices have been set up correctly. You might want to check manually the logFC result against the actual result for a few genes, i.e., calculating mean log intensities and then subtracting the reference from the treated group value. Best, Saroj biosciencegeek at gmail.com wrote: > Hi, > I have searched the mailing list but have found no solution.I have a set of > 19 genes from two cancer types from a single dye experiment that have been > analysed by limma. How do I know by looking at the logFC values which genes > have been upregulated and downregulated? > > *Gene logFC adjusted p value* > 1 4.503176282 8.16484E-07 > 2 3.098042379 0.001186095 > 3 2.478184614 6.25887E-06 > 4 2.123900966 0.000345836 > 5 2.072218463 0.000307254 > 6 1.861216801 0.019495491 > 7 1.60330851 0.000170216 > 8 1.371819046 0.041850715 > 9 1.32421397 0.002931049 > 10 1.290754778 1.6091E-05 > 11 1.110357905 0.011299876 > 12 -0.638346118 0.046342014 > 13 -0.661346419 0.019450208 > 14 -0.67761362 0.046342014 > 15 -0.90175871 0.020400911 > 16 -0.904514183 0.014558953 > 17 -1.015572133 0.046342014 > 18 -1.545921472 5.24644E-05 > 19 -3.499508887 1.58919E-06 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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> i.e., calculating mean log intensities and then subtracting the > reference from the treated group value. > I meant subtracting the reference cancer from the other cancer group value. > Best, > > Saroj > > biosciencegeek at gmail.com wrote: >> Hi, >> I have searched the mailing list but have found no solution.I have a >> set of >> 19 genes from two cancer types from a single dye experiment that have >> been >> analysed by limma. How do I know by looking at the logFC values which >> genes >> have been upregulated and downregulated? >> >> *Gene logFC adjusted p value* >> 1 4.503176282 8.16484E-07 >> 2 3.098042379 0.001186095 >> 3 2.478184614 6.25887E-06 >> 4 2.123900966 0.000345836 >> 5 2.072218463 0.000307254 >> 6 1.861216801 0.019495491 >> 7 1.60330851 0.000170216 >> 8 1.371819046 0.041850715 >> 9 1.32421397 0.002931049 >> 10 1.290754778 1.6091E-05 >> 11 1.110357905 0.011299876 >> 12 -0.638346118 0.046342014 >> 13 -0.661346419 0.019450208 >> 14 -0.67761362 0.046342014 >> 15 -0.90175871 0.020400911 >> 16 -0.904514183 0.014558953 >> 17 -1.015572133 0.046342014 >> 18 -1.545921472 5.24644E-05 >> 19 -3.499508887 1.58919E-06 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > -------------------------------------------------------------------- ---- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Thanks a million. Simple question but I couldn't get the answer. Very kind of you, Saroj. Regards Eamonn 2009/5/25 Saroj K Mohapatra <saroj at="" vt.edu="">: > >> i.e., calculating mean log intensities and then subtracting the reference >> from the treated group value. >> > I meant subtracting the reference cancer from the other cancer group value. > > >> Best, >> >> Saroj >> >> biosciencegeek at gmail.com wrote: >>> >>> Hi, >>> I have searched the mailing list but have found no solution.I have a set >>> of >>> 19 genes from two cancer types from a single dye experiment that have >>> been >>> analysed by limma. How do I know by looking at the logFC values which >>> genes >>> have been upregulated and downregulated? >>> >>> *Gene logFC ? ? ? ? ? ? ?adjusted p value* >>> 1 ? ? ?4.503176282 ? ? 8.16484E-07 >>> 2 ? ? ?3.098042379 ? ? 0.001186095 >>> 3 ? ? ?2.478184614 ? ? 6.25887E-06 >>> 4 ? ? ?2.123900966 ? ? 0.000345836 >>> 5 ? ? ?2.072218463 ? ? 0.000307254 >>> 6 ? ? ?1.861216801 ? ? 0.019495491 >>> 7 ? ? ?1.60330851 ? ? ? 0.000170216 >>> 8 ? ? ?1.371819046 ? ? 0.041850715 >>> 9 ? ? ?1.32421397 ? ? ? 0.002931049 >>> 10 ? ? 1.290754778 ? ?1.6091E-05 >>> 11 ? ? 1.110357905 ? ?0.011299876 >>> 12 ? ? -0.638346118 ? 0.046342014 >>> 13 ? ? -0.661346419 ? 0.019450208 >>> 14 ? ? -0.67761362 ? ? 0.046342014 >>> 15 ? ? -0.90175871 ? ? 0.020400911 >>> 16 ? ? -0.904514183 ? 0.014558953 >>> 17 ? ? -1.015572133 ? 0.046342014 >>> 18 ? ? -1.545921472 ? 5.24644E-05 >>> 19 ? ? -3.499508887 ? 1.58919E-06 >>> >>> ? ?[[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- All the Best, Eamonn
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