Hi Jason,

Thanks for the hint. You were correct. Apparently no genes passes the
p-value threshold of 0.05, which is to be expected, when doing an analysis
of only two samples with no replica. I didn't think about that factor, as
the error message is very encrypted.
I think there should be a better message there - something like " no genes
passes the threshhold of the given p-value". This should be checked, before
the command try to convert the 'fit' Object into a data.frame with no genes
in it and than do the images.

Anyhow, thanks again for this (obvious :( ) comment

Assa


On Thu, Jun 12, 2014 at 12:20 AM, Jason Hackney <hackney.jason@gene.com>
wrote:

> Hi Assa,
>
> A couple of questions/comments:
>
> 1. How many features pass your p-value cutoff of 0.05?
> 2. Could you provide your sessionInfo, so I can see what version of
> ReportingTools you're using?
>
> I believe the data.frame in the error message comes from the coercion of
> your DESeqResults object to a data.frame before being formatted as an html
> table. This happens in two steps for this type of object: First, the
> results are made into a data.frame, optionally including annotations (using
> the toReportDF method); second, plots and optionally links are added to the
> data.frame (using the modifyReportDF method).
>
> My further guess about what's going wrong here is that there is something
> going wrong in making the plots for the individual genes. You could test
> this by adding the parameter make.plots = FALSE to your publish call.
> This might not throw the same error.
>
> At the very least, it looks like there's a bug in the modifyReportDF
> method(s) being used that don't correctly check for zero row input, so I'll
> include a fix for that with a more helpful error.
>
> Thanks!
>
> J
>
>
>
>
>
> On Wed, Jun 11, 2014 at 1:31 PM, Assa Yeroslaviz <frymor@gmail.com> wrote:
>
>> Hi,
>>
>> I am running (again) a DESeq analysis and try to create a html report
>> using
>> the ReportingTools package.
>>
>> I do the DESeq2 analysis and get the fit object like in the manual (see
>> below). I than try to create the html report but keep getting an error I
>> can't interpret.
>>
>> Error in `$<-.data.frame`(`*tmp*`, "Image", value = "<a
>> href=\"figuresDEgenes_IFM_0_3dvsleg/boxplot..pdf\"><img border=\"0\"
>> src=\"figuresDEgenes_IFM_0_3dvsleg/mini..png\"
>> alt=\"figuresDEgenes_IFM_0_3dvsleg/mini..png\"></img></a>") :
>>   replacement has 1 row, data has 0
>>
>> I really don't understand what data.frame is meant here.
>>
>> In the DEseq analysis I don't have any replica, only two samples, which I
>> ran with this code:
>> FirstComp <- Table[,c(5,8)]
>> > head(FirstComp)
>>                 WT  treated
>> FBgn0000003        0    7
>> FBgn0000008       92 2096
>> FBgn0000014       32   23
>> FBgn0000015       13   21
>> FBgn0000017      652 2782
>> FBgn0000018       51  139
>> colData1 <- data.frame(row.names=names(FirstComp), condition = c("WT",
>> "treated"))
>>
>> cds <- DESeqDataSetFromMatrix (
>>     countData =     FirstComp,
>>     colData   =     colData1,
>>     design    = ~    condition
>>     )
>>
>> class: DESeqDataSet
>> dim: 14869 2
>> exptData(0):
>> assays(1): counts
>> rownames(14869): FBgn0000003 FBgn0000008 ... FBgn0261574 FBgn0261575
>> rowData metadata column names(0):
>> colnames(2): WT treated
>> colData names(1): condition
>>
>> fit = DESeq(cds)
>> res = results(fit)
>>
>> After that I try to create the html report with these commands:
>> des2Report <- HTMLReport()
>> publish(fit,des2Report, pvalueCutoff=0.05,annotation.db=NULL, factor =
>> colData(fit)$condition)
>> finish(des2Report)
>>
>> Than I keep getting the above mentioned error message.
>>
>> Can anyone explain to me what I am doing wrong?
>>
>> thanks
>> Assa
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>
>
>
> --
> Jason A. Hackney, Ph.D.
> Bioinformatics and Computational Biology
> Genentech
> hackney.jason@gene.com
> 650-467-5084
>
>
>

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