User: Sermsawat Tunlaya-anukit

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Posts by Sermsawat Tunlaya-anukit

<prev • 9 results • page 1 of 1 • next >
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How to design matrix that account to effect of transgenic event in edgeR ?
... I would like to ask about design matrix in GLM model in edgeR. I have group of transgenic down regulate gene. We have 3 lines of transgnics per down regulate gene which different level (event) of down regulate gene and in each line we have 3 replicate. This means we have 9 sample per 1 gene downregu ...
edger written 5.9 years ago by Sermsawat Tunlaya-anukit90
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CQN normalization
... I would like to normlization populus RNA seq with package CQN. I follow the code as show in manual, but after run i got the RPKM as minus(see detail below). What is the meaning of minus in RPKM? Or i done something wrong in my code? I try to visulize with cqn plot, and i think my data are not bias b ...
cqn written 6.1 years ago by Sermsawat Tunlaya-anukit90 • updated 6.1 years ago by Kasper Daniel Hansen6.4k
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Answer: A: How to output the graphs generated during edgeR analysis to pdf file
... Did you try to use Rstudio http://rstudio.org/ ? It is very convenient to export graphs in pdf or other format. Sermsawat T. On Thu, Apr 19, 2012 at 3:23 PM, Javerjung Sandhu wrote: > Hi List, > I just want to know how to output the graphs generated during edgeR > analysis to pdf file. ...
written 6.3 years ago by Sermsawat Tunlaya-anukit90
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Comment: C: question about normalization of RNAseq by tweeDEseq using TMM from edgeR
... Thank you for your answer. I just want to find normalization count for another analysis such as partial correlation. I used edgeR for calculate differential gene expression. I calculate normalize count by using raw count divide by effective library size (normalize factor multiple with library size) ...
written 6.5 years ago by Sermsawat Tunlaya-anukit90
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question about normalization of RNAseq by tweeDEseq using TMM from edgeR
... I have some question about normalization in package tweeDEseq which using TMM method in edgeR to normalize count data. I run normalization as manual and found something unusual. The read count before normalization of gene 4 sample X1 and X2 is 0, but after normalization it turn to 4 and 3. Why norma ...
normalization edger tweedeseq written 6.5 years ago by Sermsawat Tunlaya-anukit90 • updated 6.5 years ago by Robert Castelo2.2k
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edgeR: exactTest different p value in new version 2.4
... I used edgeR to test differential expression of RNA seq data, but i noticed some different between old version 2.2.5and new version2.4. I compare p value and adjust p value between old version and new one using exactTest() and found that the values are slightly different(logFC and LogConc are the sa ...
edger written 6.8 years ago by Sermsawat Tunlaya-anukit90 • updated 6.7 years ago by Gordon Smyth34k
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Comment: C: edgeR : How to associated trait with DE?
... I would like to make sure about interpretation of GLM associated with trait in edgeR. From my design matrix with associate with trait that i interest. GLM will answer question that which gene is associated with my trait under condition 3 factor that i put into design matrix. What is model equation f ...
written 6.9 years ago by Sermsawat Tunlaya-anukit90
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Comment: C: edgeR : How to associated trait with DE?
... Thank you very much for code example. some traits i measure and has technical replicate can i assign those data into design metrics or i just use mean. Best regards, Sermsawat T. On Sep 15, 2011, at 1:22 AM, Gordon K Smyth wrote: > Dear Sermsawat, > > NAs are not permitted in design matri ...
written 6.9 years ago by Sermsawat Tunlaya-anukit90
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edgeR : How to associated trait with DE?
... Can i associated trait into edgeR result? I have quantitative traits such as height in each library that would like to find gene that co- regulate or co-expression with that trait. How can i apply this into edgeR? Can i use $psedo.alt to calculate correlation with my trait? Or i should GLM to calcul ...
edger written 6.9 years ago by Sermsawat Tunlaya-anukit90 • updated 6.9 years ago by Gordon Smyth34k

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