Question: How can I select the top up- and down-regulated genes from more than 8000 DEG in microarray set
0
gravatar for AAhmed
2.8 years ago by
AAhmed20
AAhmed20 wrote:

I am using microarray (GSE38642) database,that includes 54 non-diabetic and 9 diabetic islets samples, platform ( Affymetrix Human Gene 1.0 ST Array). I used Bioconductor to mining the data and I got 8500 DEGs. Now I want to select the top up- and down-regulated genes. I am not sure what I have to do for example I used: FC_thresh = 10 and pvalue_thresh= 1.2e-8 to selcet the top up-regulated genes according to the formula:

(DES>=FC_thresh && DES<pvalue_thresh).

what have I done with down-regulated?

I am new in this field. any help will be highly appreciated

gene • 868 views
ADD COMMENTlink modified 2.8 years ago by Devon Ryan89k • written 2.8 years ago by AAhmed20
1

you could have the same cut off for down regulated genes as well with negative fold change. DES<= -10 && DES<pvalue_thresh

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Prasad1.5k
1
gravatar for Devon Ryan
2.8 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:
  1. Ensure you're filtering on the adjusted p-value, rather than the raw p-value.
  2. Take the absolute value (abs()) of the fold change. Then you have less typing and will always get the top genes in each direction.
ADD COMMENTlink written 2.8 years ago by Devon Ryan89k

Could you clarify a little bit how can I filter on the adjusted p-value? They are equal (p-value=adjusted p-value)

        logFC AveExpr      t    P.Value  adj.P.Val      B
8040338 13.171  13.175 408.57 2.194e-114 2.194e-114 243.97
8153903 12.281  12.300 395.29 1.955e-113 1.955e-113 242.32
7895588 12.150  12.132 390.52 4.371e-113 4.371e-113 241.71
7892902 13.140  13.143 378.48 3.473e-112 3.473e-112 240.11
7895610 11.531  11.527 373.39 8.514e-112 8.514e-112 239.42
8177732 12.529  12.519 372.59 9.820e-112 9.820e-112 239.30
7896050 12.867  12.855 370.93 1.318e-111 1.318e-111 239.07
7896349 12.121  12.133 368.41 2.072e-111 2.072e-111 238.72
7892509 12.027  12.038 367.11 2.619e-111 2.619e-111 238.53
7894666 11.718  11.729 366.33 3.013e-111 3.013e-111 238.42
8179041 12.541  12.533 365.72 3.366e-111 3.366e-111 238.34
7935320 11.418  11.417 363.72 4.840e-111 4.840e-111 238.05
8164060 12.564  12.566 363.21 5.307e-111 5.307e-111 237.98
7893345 12.606  12.601 361.74 6.945e-111 6.945e-111 237.76
7893316 12.573  12.578 361.41 7.371e-111 7.371e-111 237.72
7892829 11.970  11.975 359.39 1.068e-110 1.068e-110 237.42
8119993 12.127  12.135 357.49 1.517e-110 1.517e-110 237.14
8110022 11.298  11.294 357.33 1.564e-110 1.564e-110 237.12
7987449 10.551  10.549 356.89 1.696e-110 1.696e-110 237.06
7895547 11.805  11.798 356.33 1.884e-110 1.884e-110 236.97
7893530 11.930  11.936 355.86 2.056e-110 2.056e-110 236.90
7895320 11.603  11.589 354.20 2.801e-110 2.801e-110 236.66
7895475 12.724  12.721 353.71 3.067e-110 3.067e-110 236.58
8085026 11.892  11.896 353.59 3.136e-110 3.136e-110 236.56
7893015 12.123  12.131 353.17 3.394e-110 3.394e-110 236.50
7894236 12.432  12.429 353.00 3.507e-110 3.507e-110 236.48
7894991 12.363  12.344 352.06 4.181e-110 4.181e-110 236.33
7894098 12.835  12.829 351.81 4.385e-110 4.385e-110 236.30
8061136 12.390  12.428 350.77 5.333e-110 5.333e-110 236.14
7894596 11.619  11.633 349.11 7.304e-110 7.304e-110 235.89
8117777 11.286  11.279 349.03 7.416e-110 7.416e-110 235.87
7895484 11.300  11.304 348.58 8.066e-110 8.066e-110 235.81
7893264 12.364  12.370 348.53 8.147e-110 8.147e-110 235.80
8169740 11.351  11.349 348.38 8.379e-110 8.379e-110 235.78
7918825 12.042  12.030 347.97 9.056e-110 9.056e-110 235.71
7895317 12.159  12.176 347.88 9.219e-110 9.219e-110 235.70
7910124 10.923  10.922 346.46 1.209e-109 1.209e-109 235.48
7896438 11.940  11.939 346.01 1.318e-109 1.318e-109 235.41

@Devon

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by AAhmed20
1

This is the first case I have ever seen where raw and adjusted p-values are the same. That's incredibly unusual and I would recommend double checking that (use the p.adjust() function) to make sure they're correct.

ADD REPLYlink written 2.8 years ago by Devon Ryan89k
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 2.3.0
Traffic: 1847 users visited in the last hour