Question: Microarray processed data: Cut off
0
gravatar for tungon
2.6 years ago by
tungon0
tungon0 wrote:

Hi all, 

I am new in here and have some questions about array analysis.

1. How can I make a cut-off in a processed micro-array?

2. If I found a specific cut-off in one specific gene for analysis, do I need to use the same cut off for the whole data set, if I want to compare with the other genes?

Thanks

 

rna-seq • 1.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by tungon0
1

Regarding question (1) - take a look at the "similar posts" listed on the right hand side of the page here - there are good answers on those threads about possible data filters, for example Microarray Data: Intensity Cutoff

Regarding question (2) - possibly, but it depends on what type of cut-off you are thinking of - an intensity cutoff?  An Affymetrix A/P call cutoff?  Or a statistic-based cutoff (like an adjusted p-value from a T-test)?

The answer depends on what type of microarray you are using.  If you provide that information, others could give you more detailed advice.

 

ADD REPLYlink written 2.6 years ago by Ahill920

Thank you for your help. I will look further about the old posts.

I am analysing the normalised data from whole-Genome DASL HT Assay, illumina and I think I am using a statistic-based cut-off. The array value ranging from 6.6 - 15.

For example, the cut-off from a specific gene A in 9 has statistically significant and gene B in 10 has statistically significant. Do I need to keep the cut-off 9 or 10 for further gene-gene inter-reaction analysis, or other value cut-off (present / absent) I should use? 

ADD REPLYlink written 2.6 years ago by tungon0

what are the numbers you mentioned (6.6-15 range and 9, 10)? can you paste some of those data here (10-20 lines) so that we can have a look? I have a feeling that as Ahill mentioned is a p.value based cutoff (or adjusted p.value) but as the post is written it's pretty hard to say.

ADD REPLYlink written 2.6 years ago by TriS3.0k
0
gravatar for tungon
2.6 years ago by
tungon0
tungon0 wrote:

For example, gene A cut-off is 10.7537. I want to use gene A to compare with gene B,C D... in the array data,hence, should I use the gene A cut-off for all the data set, or using other cut-off (such as mid-point or average from the whole data), for chi-square  calculation? 

I don't have any experience to handle array data, hope someone can help me, thanks. 

A B C D E F H
6.8189 13.0030 8.6803 10.8104 9.5281 11.6192 7.1449
7.9735 13.3488 9.6836 11.0574 7.8270 11.0267 6.9630
7.9847 13.1529 8.9669 11.0566 10.5105 10.1033 6.8814
8.6803 13.2476 7.9847 11.2119 10.4203 11.3937 7.0782
8.8414 7.0880 13.1466 10.9931 6.7923 11.2176 6.7820
9.0455 9.6054 13.2458 10.9381 7.4185 11.4213 7.0444
9.7937 8.9361 13.3972 6.9561 10.3311 10.2571 6.9319
10.3126 7.3138 13.3550 7.1564 7.0120 12.1360 10.9988
10.7537 7.6823 13.1720 6.7970 8.7083 11.8906 10.9523
10.7799 7.3751 13.3529 6.8419 8.4394 11.1961 11.0398
10.8189 7.9735 13.4438 7.7458 9.0455 11.6035 11.0252
11.0252 7.8044 13.5171 11.1341 9.0650 11.3855 11.0194
11.7450 7.7662 13.4604 10.9341 7.0559 12.4262 8.7895
12.7937 7.9735 13.3368 11.1066 9.9627 11.9987 8.4371
13.5306 7.7620 13.2156 10.7855 6.9055 12.1645 7.0442
13.5854 7.8120 13.3886 10.8021 6.9668 11.4794 6.9840
13.6758 7.4405 13.3740 10.6626 7.2063 12.0295 8.3033
14.8189 9.1630 13.5982 9.0114 7.1289 11.7442 6.9820
14.9548 7.7369 13.5918 10.6889 8.7099 11.5042 7.0968
ADD COMMENTlink written 2.6 years ago by tungon0

ok, I'm a bit confused, why do you want to do chi square? you need a contingency table for chi-square, I'm not sure that's what you want.

1) how did you get the 10.7537 as cutoff?

2) is you question: "is gene A expression differnt from B, C, etc etc?

3) I assume that in the matrix you posted the columns are genes and rows are samples?

ADD REPLYlink written 2.6 years ago by TriS3.0k
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