[BioC] DEXSeq: PlotMA issues

[Alejandro Reyes]

Dear Margaret,

Could you please add the first lines of your res1 object (e.g. head)?

Best regards,
Alejandro

> Dear Alejandro,
>
> I have been having success with the pasilla exercise, but have noticed 
> that plotMA
> does not output the same graph as what is depicted in the vignette.
>
> I've tried the plotMA code after loading DEXSeq and DESeq but the 
> graph appears the same,
> the warning message is the same too.
>
> plotMA code with warning:
>
>       > plotMA(with(res1, data.frame(baseMean = meanBase,
>
> +                                  log2FoldChange = 
> ‘log2fold(untreated/treated)’,
>
> +                                  padj = padjust)),
>
>             + ylim=c(-4,4), cex= 0.8)
>
> Warning messages:
>
> 1: In Ops.factor(mmm, each) : > not meaningful for factors
>
> 2: In Ops.factor(py, ylim[1]) : < not meaningful for factors
>
>
>
> Inline image 1
> Thanks,
> ML
>
>
> On Sun, Jun 2, 2013 at 3:06 AM, Alejandro Reyes 
> <alejandro.reyes at embl.de <mailto:alejandro.reyes at embl.de>> wrote:
>
>     Dear Margaret,
>
>     The error is because you are only using one file, and I agree that
>     the error message should be more informative.
>
>     What do you intend to do with DEXSeq using only one sample? DEXSeq
>     is designed to identify differences in exon usage of at least two
>     conditions with samples with replicates (which means that you need
>     a minimum of 4 files with counts).
>
>     Best regards,
>     Alejandro
>
>         Hi-
>
>         I have a new DEXSeq error that I could use help with:
>
>             samples=data.frame(
>
>         + condition=c(rep("myfile", 1)),
>         + row.names=file.path("/home/mlinan", pattern="myfile.counts"),
>         + stringAsFactors=FALSE,
>         + check.names= FALSE)
>
>             ecs = read.HTSeqCounts(countfiles = rownames(samples),
>             design=samples,
>
>         + flattenedfile=file.path("/home/mlinan", "myfile.gff")
>         + )
>         Error in strsplit(rownames(dcounts), ":") : non-character argument
>
>             sessionInfo()
>
>         R version 3.0.1 (2013-05-16)
>         Platform: x86_64-unknown-linux-gnu (64-bit)
>
>         locale:
>         [1] C
>
>         attached base packages:
>         [1] parallel  stats     graphics  grDevices utils   datasets
>          methods
>         [8] base
>
>         other attached packages:
>         [1] DEXSeq_1.6.0       Biobase_2.20.0 BiocGenerics_0.6.0
>
>         loaded via a namespace (and not attached):
>           [1] Biostrings_2.28.0    GenomicRanges_1.12.4 IRanges_1.18.1
>           [4] RCurl_1.95-0.1.2     Rsamtools_1.12.3 XML_3.96-1.1
>           [7] biomaRt_2.16.0       bitops_1.0-5 hwriter_1.3
>         [10] statmod_1.4.17       stats4_3.0.1 stringr_0.6.2
>         [13] zlibbioc_1.6.0
>
>         My count file does have " : " symbol, here is a brief example:
>         ENSMMUG00000098993:001 0
>         ENSMMUG00000098994:001 0
>         _ambiguous 3145
>         _empty 2488107
>         _lowaqual 479881
>         _notaligned 0
>
>         Thanks,
>         Margaret Linan
>
>                 [[alternative HTML version deleted]]
>
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