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

[Gordon K Smyth]

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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