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 and...{{dropped}}

At 05:47 PM 26/07/2004, Adrian Peres wrote: >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? You are asking whether there is some rule that every microarray experiment must lead to significant differentially expressed genes. The answer is no. Some suggestions: check that you have the treatments in your targets file set up correctly; try the same analysis again without background correction; change to "fdr" instead of "holm" multiplicity adjustment; check your data quality. Gordon >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