Question: Limma or something else ? plus Normalization question
0
gravatar for Phguardiol@aol.com
15.9 years ago by
Phguardiol@aol.com720 wrote:
Hi, let say I have 9 chips (Affy U133A) A1, A2, A3 triplicates = group A B1, B2, B3 triplicates = group B C1, C2, C3 triplicates = group C I d like to know what are the genes differentially expressed between A & B, A & C, B & C I see two options (1) comparing 2 by 2 these groups using for instance LPE or another test like this one, option (2) using Limma. What would be the best option ? I like using LPE since it is well designed for low replicates. If I use option (1) should I normalize all the chips during the same process or first normalize group A with group B and run the comparison..etc ? My concern here is that I will use a relatively low number of chips with RMA / Quantile normalization, in the other way (normalizing everything at the same time) I could introduce "a bias" that is not needed. Any comments is apppreciated as usual.Thanks Philippe
limma lpe process • 549 views
ADD COMMENTlink modified 15.9 years ago by Gordon Smyth38k • written 15.9 years ago by Phguardiol@aol.com720
Answer: Limma or something else ? plus Normalization question
0
gravatar for Gordon Smyth
15.9 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:
At 02:47 AM 29/09/2003, Phguardiol@aol.com wrote: >Hi, >let say I have 9 chips (Affy U133A) >A1, A2, A3 triplicates = group A >B1, B2, B3 triplicates = group B >C1, C2, C3 triplicates = group C > >I d like to know what are the genes differentially expressed between A & >B, A & C, B & C >I see two options (1) comparing 2 by 2 these groups using for instance LPE >or another test like this one, Please explain what LPE is. > option (2) using Limma. >What would be the best option ? I like using LPE since it is well designed >for low replicates. If I use option (1) should I normalize all the chips >during the same process or first normalize group A with group B and run >the comparison..etc ? My concern here is that I will use a relatively low >number of chips with RMA / Quantile normalization, in the other way >(normalizing everything at the same time) I could introduce "a bias" that >is not needed. >Any comments is apppreciated as usual.Thanks >Philippe
ADD COMMENTlink written 15.9 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: 139 users visited in the last hour