Question: A question about MAS5 vs RMA vs GCRMA
0
gravatar for YUK FAI LEUNG
15.2 years ago by
YUK FAI LEUNG140
YUK FAI LEUNG140 wrote:
Hi there, I am helping my friend to do some analysis on his affy data. He has a simple 2x2 factorial experiment without any replication, i.e. only 4 chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw data with the default settings, and compute the fold changes of individual factor comparison. I am suprised to see that there are many more genes which have >= 2 fold change in MAS5 compare to the other two algorithms. For example in one comparison, MAS5 gives 21477 genes >= 2 fold, while RMA gives 0 and GCRMA gives 4. While I do know that RMA gives less significant genes, I do not expect to see such a drastic difference. Especially when his experiment is a drug treatment on a cell culture which is known to change a lot of genes, I am expecting to see a lot of changes even in the fold change comparison. Is this discrepancy occured due to the lack of replication? Regards, Fai -- Yuk Fai Leung Department of Molecular and Cellular Biology Harvard University BL 2079, 16 Divinity Avenue Cambridge, MA 02138 Tel: 617-495-2599 Fax: 617-496-3321 email: yfleung@mcb.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com
affy gcrma • 1.8k views
ADD COMMENTlink modified 15.2 years ago by Martino Barenco110 • written 15.2 years ago by YUK FAI LEUNG140
Answer: A question about MAS5 vs RMA vs GCRMA
0
gravatar for Adaikalavan Ramasamy
15.2 years ago by
Adaikalavan Ramasamy1.8k wrote:
In BioConductor, the rma and gcrma expression measures are log2 transformed while MAS 5.0 is not. Could this be your reason ? Regards, Adai On Mon, 2004-09-13 at 15:48, YUK FAI LEUNG wrote: > Hi there, > > I am helping my friend to do some analysis on his affy data. He has a > simple 2x2 factorial experiment without any replication, i.e. only 4 > chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw > data with the default settings, and compute the fold changes of > individual factor comparison. I am suprised to see that there are many > more genes which have >= 2 fold change in MAS5 compare to the other two > algorithms. For example in one comparison, MAS5 gives 21477 genes >= 2 > fold, while RMA gives 0 and GCRMA gives 4. > > While I do know that RMA gives less significant genes, I do not expect > to see such a drastic difference. Especially when his experiment is a > drug treatment on a cell culture which is known to change a lot of > genes, I am expecting to see a lot of changes even in the fold change > comparison. Is this discrepancy occured due to the lack of replication? > > Regards, > Fai
ADD COMMENTlink written 15.2 years ago by Adaikalavan Ramasamy1.8k
Adai, Thanks! I did not notice that. I have never used MAS5 in Bioc. After correcting for this error, and using the P calls, the number of genes >= 2 fold equals to 147. Best regards, Fai Adaikalavan Ramasamy wrote: > In BioConductor, the rma and gcrma expression measures are log2 > transformed while MAS 5.0 is not. Could this be your reason ? > > Regards, Adai > > > On Mon, 2004-09-13 at 15:48, YUK FAI LEUNG wrote: > >>Hi there, >> >>I am helping my friend to do some analysis on his affy data. He has a >>simple 2x2 factorial experiment without any replication, i.e. only 4 >>chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw >>data with the default settings, and compute the fold changes of >>individual factor comparison. I am suprised to see that there are many >>more genes which have >= 2 fold change in MAS5 compare to the other two >>algorithms. For example in one comparison, MAS5 gives 21477 genes >= 2 >>fold, while RMA gives 0 and GCRMA gives 4. >> >>While I do know that RMA gives less significant genes, I do not expect >>to see such a drastic difference. Especially when his experiment is a >>drug treatment on a cell culture which is known to change a lot of >>genes, I am expecting to see a lot of changes even in the fold change >>comparison. Is this discrepancy occured due to the lack of replication? >> >>Regards, >>Fai > > > -- Yuk Fai Leung Department of Molecular and Cellular Biology Harvard University BL 2079, 16 Divinity Avenue Cambridge, MA 02138 Tel: 617-495-2599 Fax: 617-496-3321 email: yfleung@mcb.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com
ADD REPLYlink written 15.2 years ago by YUK FAI LEUNG140
Answer: A question about MAS5 vs RMA vs GCRMA
0
gravatar for Martino Barenco
15.2 years ago by
Martino Barenco110 wrote:
Dear Fai, I think justRMA() (If this is what you used) returns 2-log transformed values so that to >=2 fold changes correspond to (absolute difference)>=1 in that metric. Bests Martino On Monday, September 13, 2004, at 03:48 PM, YUK FAI LEUNG wrote: > Hi there, > > I am helping my friend to do some analysis on his affy data. He has a > simple 2x2 factorial experiment without any replication, i.e. only 4 > chips. Because of this, I just perform MAS5, RMA and GCRMA on the raw > data with the default settings, and compute the fold changes of > individual factor comparison. I am suprised to see that there are many > more genes which have >= 2 fold change in MAS5 compare to the other > two algorithms. For example in one comparison, MAS5 gives 21477 genes > >= 2 fold, while RMA gives 0 and GCRMA gives 4. > > While I do know that RMA gives less significant genes, I do not expect > to see such a drastic difference. Especially when his experiment is a > drug treatment on a cell culture which is known to change a lot of > genes, I am expecting to see a lot of changes even in the fold change > comparison. Is this discrepancy occured due to the lack of > replication? > > Regards, > Fai > -- > Yuk Fai Leung > Department of Molecular and Cellular Biology > Harvard University > BL 2079, 16 Divinity Avenue > Cambridge, MA 02138 > Tel: 617-495-2599 > Fax: 617-496-3321 > email: yfleung@mcb.harvard.edu; yfleung@genomicshome.com > URL: http://genomicshome.com > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > --------------------------------------- Martino Barenco CoMPLEX 4, Stephenson Way London NW1 2HE Tel.: +44 20 7679 5088 Fax.: +44 20 7679 5052 (please specify "CoMPLEX") Email: m.barenco@ucl.ac.uk
ADD COMMENTlink written 15.2 years ago by Martino Barenco110
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: 189 users visited in the last hour