[BioC] edgeR : How to associated trait with DE?

[Sermsawat Tunlaya-anukit]

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 matrices in edgeR.  If you have NAs, you have to remove these libraries explicitly:
> 
>  i <- !is.na(Growth64)
>  disph64 <- estimateGLMCommonDisp(d[,i], design[i,])
> 
> Best wishes
> Gordon
> 
> 
> On Wed, 14 Sep 2011, Sermsawat Tunlaya-anukit wrote:
> 
>> Thank you for your recommend. I also have some trait which has missing data (NA). Do edgeR estimateGLMcommonDisp has any option that skip this missing data? I try na.rm=TRUE but it isn't help.
>> 
>> 
>>> design <- model.matrix(~group,data=d$samples)
>>> designh64 <- cbind(design,Growth64)
>>> designh64
>>       (Intercept) group2 group3 group4 Growth64
>> Rwt_2             1      0      0      0       48
>> Rwt_3             1      0      0      0       NA
>> Rwt_4             1      0      0      0       NA
>> RL4_3_1           1      1      0      0       32
>> RL4_4_2           1      1      0      0       15
>> RL4_5_1           1      1      0      0       22
>> RL4_6_2           1      1      0      0       25
>> RL7_1_2           1      0      1      0       15
>> RL7_2_3           1      0      1      0       10
>> RL7_3_1           1      0      1      0       12
>> RL8_3_1           1      0      0      1       12
>> RL8_3_2           1      0      0      1       12
>>> disph64<-estimateGLMCommonDisp(d,designh64)
>> Error in qr.default(X) : NA/NaN/Inf in foreign function call (arg 1)
>>> 
>>> disph64<-estimateGLMCommonDisp(d,designh64, na.rm=TRUE)
>> Error in dispCoxReid(y, design, offset = offset, ...) :
>> unused argument(s) (na.rm = TRUE)
>> 
>> Sermsawat Tun.
>> 
>> 
>> On Sep 14, 2011, at 7:01 PM, Gordon K Smyth wrote:
>> 
>>> Dear Sermsawat,
>>> 
>>> In edgeR, you can simply add a quantitative column to the design matrix, then use glmFit() and glmLRT() to test for the significance of the coefficient for that column.
>>> 
>>> I do not recommend that you do the calculations using the pseudo counts.
>>> 
>>> Best wishes
>>> Gordon
>>> 
>>>> Date: Tue, 13 Sep 2011 23:01:29 -0400
>>>> From: Sermsawat Tunlaya-anukit <stunlay at ncsu.edu>
>>>> To: bioconductor at r-project.org
>>>> Subject: [BioC] 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 calculate DE that associated with trait? I am not sure how to apply my trait into design or another vector and calculate estimateGLMCommonDisp.
>>>> 
>>>> Thank in advance,
>>>> Sermsawat Tunlaya-anukit
>>> 
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>> 
> 
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