[BioC] edgeR : How to associated trait with DE?
Gordon K Smyth
smyth at wehi.EDU.AU
Thu Sep 22 01:01:17 CEST 2011
Dear Sermsawat,
Technical replicates should be aggregated by summing, not by taking the
mean.
Best wishes
Gordon
---------------------------------------------
Professor Gordon K Smyth,
Bioinformatics Division,
Walter and Eliza Hall Institute of Medical Research,
1G Royal Parade, Parkville, Vic 3052, Australia.
Tel: (03) 9345 2326, Fax (03) 9347 0852,
smyth at wehi.edu.au
http://www.wehi.edu.au
http://www.statsci.org/smyth
On Wed, 21 Sep 2011, Sermsawat Tunlaya-anukit wrote:
> 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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