Dear all,

I am using HTqPCR to analyse different expression of miRNAs, where I am
comparing two treatments, 1 with 2 biological replicates and the second with
2 biological replicates

I have followed the vignete, read the files, made raw.cat and filtered out
IQR<1.5 and category= undetermined and type=endogenous
 and everything went well until the fit test:

qDE.limma<-limmaCtData(iqr.filt, design=design, contrasts=contrasts,
ndups=2, spacing=1)
Error in dim(M) <- c(spacing, ndups, ngroups, nslides) :
  dims [product 396] do not match the length of object [402]

can someone tell me what this means? it still performed the test but I would
like to clear out this.

The other weird thing is the result of the test:

   genes feature.pos     t.test      p.value  adj.p.value        ddCt
meanTarget meanCalibrator categoryTarget
39   miR-122a       H7;H8  6.7414852 6.141932e-06 0.0002456773  14.8264063
34.833906      20.007500   Undetermined
1     miR-18a       A1;A2  5.5408137 5.366491e-05 0.0010732983  13.5365104
30.431094      16.894583   Undetermined
10    miR-368     B11;B12 -4.7841570 2.320152e-04 0.0030935366 -23.1045833
7.119063      30.223646   Undetermined

the feature.pos is different in both treatments but it is not, I have
checked and re-checked the files and miR-18a is in pos. A1 in all cards.

Thanks for your help.
With kind regards

Andreia
-- 
--------------------------------------------
Andreia J. Amaral
Unidade de Imunologia Clínica
Instituto de Medicina Molecular
Universidade de Lisboa
email: andreiaamaral@fm.ul.pt
         andreia.fonseca@gmail.com

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