[BioC] No $df.residual

[Johnson, Franklin Theodore]

Dear Sean Davis,

Thanks for the input.

I took the average of the RMA normalized values for each genotype. Then, log2 transformed as below:

The raw data is from NimbleGen array custom-designed for apple genome.
It was normalized using RMA method. This was downloaded from NCBI/GEO, 
then I took log2(exprs(eset), after reading the papers and making phenoData.txt...Or, I did "log2(matrix(assayData))", then made an eset with this input file.

Anyhow, I will go back and start from the RMA normalized values and replicates.
However, for 3 reps each for 3 genotypes:
After making an eset, 
This contrast matrix:
contrastMatrix=c(0,0,1, 0,1,0, 1,0,0, 0,0,2, 0,2,0, 2,0,0, 0,0,3, 0,3,0, 3,0,0)   
should work, right? 
Or, is another format, i.e. -1,.. ; {1,1,1}, a better option for comparision?
If its 1,1,1, for one genotype, contrast with the other 2 genotypes<- still cannot get $df.residuals correct?
 Ambrosia Gala Melrose
> 1        1    0       0
> 2        1   -1       0
> 3        1    0      -1
---didn't work either---

Is there a way to coerce limma to accept a variable with only 2 levels? 
I can write an ANOVA that accepts a factor with just 1 level...it's kinda of odd I can't do this with limma.
For example, sex is M an F...only 2 levels. If I'm not mistaken, limma require 'more than 2 levels', right? 
But, limma is very useful, and efficient.    

Hope this helps...I'm here all night! 
Regards,
Franklin  


________________________________________
From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov]
Sent: Tuesday, May 07, 2013 3:12 PM
To: FRANKLIN JOHNSON [guest]
Cc: bioconductor at r-project.org; franklin.johnson at wsu.edu
Subject: Re: [BioC] No $df.residual

Hi, Franklin.  See below.

On Tue, May 7, 2013 at 6:04 PM, FRANKLIN JOHNSON [guest]
<guest at bioconductor.org> wrote:
>
> Hello,
>
> I want to determine differences between three genotypes.
> I'm using an exprs(eset).
> I made:
> contrastMatrix
> Ambrosia Gala Melrose
> 1        1    0       0
> 2        0    1       0
> 3        0    0       1
> However, in fit2()
> $df.residual
> [1] 0 0 0 0 0
> 68660 more elements ...
>
> $sigma
> [1] NA NA NA NA NA
> 68660 more elements ...
> I looked back to fit() and had the same output.
> However, my design matrix should allow me to compute differences. Does it say somewhere reps are necessary, other times seems to suggest need based on hypothesis.
>

Yes, you need replicates to have residual degrees of freedom and to
perform a statistical test.

> I already computed the average.

Might be obvious, but the average of what?

> I can also compute the stats for this as well, if needed.
> Can I create an object of this to use with limma?

Again, can your clarify what data you mean to use with limma?

Sean

> On the other hand,
> $qr
>   Ambrosia Gala Melrose
> 1       -1    0       0
> 2        0   -1       0
> 3        0    0       1
>
> Also, this contrastMatrix doesn't fit.
>
> Regards,
> Franklin
>
>
>
>
>
>
>  -- output of sessionInfo():
>
> R 2.15.1
>> objects()
>  [1] "constrast.matrix"          "contrastNames"             "contrastsMatrix"
>  [4] "design"                    "eFBestN"                   "eFBestNlog2t"
>  [7] "eSetlog2_eFBestN"          "exprs"                     "fit"
> [10] "fit2"                      "geneID"                    "HistogramPlot"
> [13] "limmaGUIenvironment"       "log2_eFBestN"              "mydesign"
> [16] "myfit"                     "NEOffsetDefault"           "numParameters"
> [19] "parameterNames"            "pDataN"                    "pDatarootstocKlog2"
> [22] "pDatarootstocNlog2"        "pDatascioNlog2"            "phenoDatN"
> [25] "SampleNames"               "scion.phenoData"           "ss.rootstock.eFBestNlog2t"
> [28] "ss.rootstock.log2"         "ss.rootstock.log2t"        "ss.scion.eFBestNlog2t"
> [31] "ss.scion.log2"             "ss.scion.log2t"            "targets"
> #####################
> function (package = NULL)
> {
>     z <- list()
>     z$R.version <- R.Version()
>     z$platform <- z$R.version$platform
>     if (nzchar(.Platform$r_arch))
>         z$platform <- paste(z$platform, .Platform$r_arch, sep = "/")
>     z$platform <- paste(z$platform, " (", 8
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor