Question: Top 50 Candidate genes: "wrong" pValues and B results!
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gravatar for James W. MacDonald
15.2 years ago by
United States
James W. MacDonald51k wrote:
Adrian, It is quite possible to get this sort of result with microarray data. First, if you only have a few replicates, the power of a t-test is pretty low so it is difficult to get any large t-statistics (although I have no idea how many replicates you have). Second, the default multiplicity adjustment for topTable is the Holm procedure, which is fairly conservative (you don't say what you used...). Third, you only have six genes in this list with a fold change greater than two-fold anyway, which indicates that there may not be any real big differences between the two samples. Note that there may be more genes with FC > 2 farther down the list, but since these will have smallish t-statistics, the fold change is likely due to an outlier or two. You may simply need to do some more microarrays in order to get enough power to detect differentially expressed genes. Alternatively, you might just try validating some of the top genes in this list and see if you see any differential expression using RTPCR or Northern blots. Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Adrian Peres <adrian.peres@cropdesign.com> 07/26/04 03:47AM >>> Hi all I am using Limma GUI to analyze Agilent data and I have some troubles. Hereafter I placed a sample of the statistic analysis that looks very strange to me! The pValues are all "1" and I don't understand why? B data are not better neither... Can my data be so bad? Greetings, Adrian M A t Pvalue B 2.099 9.493 27.16 1 -3.417 -1.389 11.37 -15.45 1 -3.437 -1.079 8.683 -15.28 1 -3.438 -1.073 8.952 -14.28 1 -3.442 0.944 6.831 12.66 1 -3.451 -0.8108 8.475 -11.51 1 -3.46 -0.7985 8.784 -11.39 1 -3.461 -0.803 12.67 -11.38 1 -3.461 -0.9375 12.22 -11.13 1 -3.463 -0.8701 10.24 -10.84 1 -3.466 -1.383 12.55 -10.63 1 -3.468 -0.846 9.56 -10.22 1 -3.473 -0.7271 11.98 -10.1 1 -3.474 0.977 8.603 9.975 1 -3.476 -0.7734 9.416 -9.716 1 -3.48 -0.975 9.89 -9.52 1 -3.482 -0.6683 7.127 -9.514 1 -3.482 -0.8116 6.528 -9.493 1 -3.483 -0.673 8.966 -9.434 1 -3.484 -0.8475 11.26 -9.125 1 -3.489 -0.8426 10.43 -9.038 1 -3.49 -0.7633 8.999 -8.977 1 -3.491 -0.8202 10.14 -8.804 1 -3.494 -0.6119 9.076 -8.671 1 -3.497 -0.7045 9.458 -8.611 1 -3.498 -0.761 10.07 -8.468 1 -3.501 -0.9212 10.8 -8.437 1 -3.502 -1.003 8.465 -8.392 1 -3.502 confidentiality notice: The information contained in this e-mail is confidential\ an...{{dropped}}
microarray gui cancer limma • 513 views
ADD COMMENTlink written 15.2 years ago by James W. MacDonald51k
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