Question: How to treat data with three biological replicates
1
gravatar for mengmpp
4.4 years ago by
mengmpp10
Ireland
mengmpp10 wrote:

Hi all,

for each point (control and treatment), I have two more biological replicates, like ,control: A0,A3,A6, treatment:A1,A4,A7. After normalized with RPKM, I got a set of data with log2(A10/A0), P-value, FDR; log2(A4/A3), P-value, FDR; and log2(A7/A6), P-value, FDR. After that, I found common genes which consistently expressed in three replicates. That is main aim I want to extract. OK, the problem is for these common gene, they have three set of data, how can I assemble to one set?

Thanks a million. 

rna-seq • 1.9k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by mengmpp10
A0-Expression A1-Expression A0-RPKM A1-RPKM log2 Ratio(A1/A0) P-value FDR A3-Expression A4-Expression A3-RPKM A4-RPKM log2 Ratio(A4/A3) P-value FDR A6-Expression A7-Expression A6-RPKM A7-RPKM log2 Ratio(A7/A6) P-value FDR
715 79 45.79892 4.967396 -3.20475 7.76E-132 1.34E-129 938 113 60.01701 7.530592 -2.99454 2.05E-155 2.88E-153 365 30 23.13004 2.03935 -3.50359 1.47E-69 1.35E-67
ADD REPLYlink written 4.4 years ago by mengmpp10

Whch method/tool did you use to get the P-value or FC ? I think you have treated them as individual samples rather than replicates. 

ADD REPLYlink written 4.4 years ago by geek_y9.4k

Yes, I got these data from company, I think they treated them as individual samples.

For Quantification of gene expression, use RPKM algorithm,

for Screening of differentially expressed genes,use Poisson distribution model

for Screening of group differentially expressed genes, use NOIseq method

ADD REPLYlink written 4.4 years ago by mengmpp10

Just try it urself with DESeq/edgeR. They are well documented.

ADD REPLYlink written 4.4 years ago by geek_y9.4k

@mengmpp did you find a solution for this ? I am facing the same problem

ADD REPLYlink written 2.7 years ago by Learner 160
0
gravatar for Ido Tamir
4.4 years ago by
Ido Tamir5.0k
Austria
Ido Tamir5.0k wrote:

How do you get a p-value and an FDR from the comparison of 2 data points? llike: 0.4 RPKM vs 4 RPKM?

Please use a tool like DESeq2 or edgeR. They do everything automatically.

http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html

ADD COMMENTlink written 4.4 years ago by Ido Tamir5.0k
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