Heidi Dvinge heidi at ebi.ac.uk
Mon May 28 10:38:05 CEST 2012

Dear Mala,

> Hello Dr. Dvinge,
> I have been using HTqPCR 1.8.0  to analyze 96 well qPCR arrays. My
> experiment has 2 time point 3hrs, 18hrs and 2 treatments CT, TC and TCATP
> (2X3 factorial design). I was able to run the analysis using limmaCtData
> and export the output file for each contrast.
> Question 2
> *************************************************************
> Is there an equivalent method like TopTable in limma to extract results
> which shows the genes that are changing across the experimental condition
> (like F-statistics in ANOVA or F.p.value in limma). We can get this
> information using the write.fit() in limma.
Actually no, I never thought about incorporating this. The standard output
gives a (slightly modified) version of the results from topTable for each
of the coefficients in contrast, as well as decideTests. But not the
output from topTableF/topTable with coef=NULL.

If this is of interest, I can add it to future versions of HTqPCR?

Alternatively, you can just extract the Ct data (using exprs or getCt) and
run lmFit/eBayes/topTableF directly. Although this of course won't take
the quality of the Ct data into account, i.e. you won't get the columns
indicating whether the target and the calibrator samples are OK or


> Runnning limmaCtData without contrast didn't help. See below
>>DE.limmaNoCtr <- limmaCtData(quan_undtrmnfilter2, design=design, ndups =
>> 1, spacing = 1)
>> write.table(qDE.limmaNoCtr, file="qDE_limmafitALL.txt", sep="\t")
> '
> Attached file for this: RCode_HTqPCR.txt ;
> limmaCtData_output_no_contrast.xls
> ***********************************************************************
> Thanks for all your help.
> Mala Sinha
> Systems Analyst
> University of Texas Medical Branch
> Galveston, Texas 77573
> masinha at utmb.edu<mailto:masinha at utmb.edu>
> (409) 747 6872

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