On Wed, Oct 17, 2012 at 10:20 AM, priya [guest] <guest@bioconductor.org>wrote:

>
> I would like to find the differentially expressed genes for several
> variables using the limma package for several groups.
>
>  -- output of sessionInfo():
>
> I have the rma normalized matrix in the following format :
>
>
> ID_REF GSM362180    GSM362181  GSM362188    GSM362189  GSM362192
> 244901 5.094871713 4.626623079 4.554272515 4.748604391 4.759221647
> 244902 5.194528083 4.985930299 4.817426064 5.151654407 4.838741605
> 244903 5.412329253 5.352970877 5.06250609  5.305709079 8.365082403
> 244904 5.529220594 5.28134657  5.467445095 5.62968933  5.458388909
> 244905 5.024052699 4.714631878 4.792865831 4.843975286 4.657188246
> 244906 5.786557533 5.242403911 5.060605782 5.458148567 5.890061836
>
> where the different columns correspond to four different types of
> promoters and each of the four promoters has a biological replicate so
> totally there are 8 columns.
>
> I tried using the Limma package to find the differentially expressed genes
> across several promoters ( with replicates) and I always get an error as
> Iam new to r and unable to understand it fully .
>
> This is the code that I used:
>
> Group <- factor(c("p1", "p1", "p2", "p2", "p3","p3","p3","p4","p4"),
> levels =
> c("GSM362180","GSM362181","GSM362188","GSM362189","GSM362192","GSM362193","GSM362194","GSM362197","GSM362198"))
>

You want:

Group <- factor(c("p1", "p1", "p2", "p2", "p3","p3","p3","p4","p4"))


>
> design <- model.matrix(~0 + Group)
>
>
The design matrix will not be correct.


> colnames(design) <-
> c("GSM362180","GSM362181","GSM362188","GSM362189","GSM362192","GSM362193","GSM362194","GSM362197","GSM362198")
>

Do not try to change the column names.


> fit <- lmFit(modified, design)
>
>
This should probably work, now.  You may need to specify a contrast matrix
to get something closer to what you want, though.

Sean



> where modified is the rma normalized data matrix as inputted in the above
> format.
> I get the following error:
>
> Coefficients not estimable: GSM362180 GSM362181 GSM362188 GSM362189
> GSM362192 GSM362193 GSM362194 GSM362197 GSM362198
> Error in lm.fit(design, t(M)) : 0 (non-NA) cases
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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