Question: Top 50 Candidate genes: "wrong" pValues and B results!
0
gravatar for Adrian Peres
15.2 years ago by
Adrian Peres30
Adrian Peres30 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? 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}}
gui limma • 412 views
ADD COMMENTlink modified 15.2 years ago by Gordon Smyth38k • written 15.2 years ago by Adrian Peres30
Answer: Top 50 Candidate genes: "wrong" pValues and B results!
0
gravatar for Gordon Smyth
15.2 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
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
ADD COMMENTlink written 15.2 years ago by Gordon Smyth38k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 281 users visited in the last hour