Hi Chao,

You can always get the sessionInfo in an R session by running the
sessionInfo() command. As for the ReportingTools error, I'm pretty sure
that the png's were included in the package. I can see them by running

$> unzip -l ReportingTools_2.4.0

The files are just misnamed in your error message:

     8777  04-12-14 09:25
extdata/csslib/images/glyphicons-halflings-white.png
    12799  04-12-14 09:25   extdata/csslib/images/glyphicons-halflings.png
      253  04-12-14 09:25   extdata/csslib/images/sort_asc.png
     1050  04-12-14 09:25   extdata/csslib/images/sort_asc_disabled.png
     1136  04-12-14 09:25   extdata/csslib/images/sort_both.png
      266  04-12-14 09:25   extdata/csslib/images/sort_desc.png
     1045  04-12-14 09:25   extdata/csslib/images/sort_desc_disabled.png

My guess is that this is a bug in ReportingTools on Windows, but I can't
confirm just yet, as I lack a test machine. I'll look into this later this
week.

As for your other error. I'm not sure what's going on, but it looks like
there's a mismatch between the rownames in your MArrayLM object (the result
of calling eBayes) and the data.frame that ReportingTools is making from
it. There are several reasons for this, but you might just check that

R> all.equal(rownames(fit2), featureNames(eset))

If this is TRUE, then I might need to do a bit more thinking about this.

Best,

Jason




On Thu, Jun 19, 2014 at 4:47 AM, 张超 <zhangchao0103@163.com> wrote:

> Hi Jason,
>
> It is very nice for you to help resolve my issues. Thanks very much.
> I have cought the session info as below. But it seems that when the
> package was installed, these pngs were not included in the downloaded
>  ReportingTools_2.4.0.zip packages. I tried to reinstall this package to
> catch the session info, but it showed that this package has been installed
> and can not be installed again. I am a new beginner of R, so could you
> please tell me what to do is helpful to you? Thanks again.
>
>
> R version 3.1.0 (2014-04-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936
> [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
> [3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936
> [4] LC_NUMERIC=C
> [5] LC_TIME=Chinese (Simplified)_People's Republic of China.936
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] ReportingTools_2.4.0       BiocInstaller_1.14.2
>  [3] knitr_1.6                  limma_3.20.5
>  [5] moex10stprobeset.db_2.14.0 org.Mm.eg.db_2.14.0
>  [7] AnnotationDbi_1.26.0       GenomeInfoDb_1.0.2
>  [9] pd.moex.1.0.st.v1_3.8.0    RSQLite_0.11.4
> [11] DBI_0.2-7                  oligo_1.28.2
> [13] Biostrings_2.32.0          XVector_0.4.0
> [15] IRanges_1.22.9             Biobase_2.24.0
> [17] oligoClasses_1.26.0        BiocGenerics_0.10.0
>
> loaded via a namespace (and not attached):
>  [1] affxparser_1.36.0         affyio_1.32.0
>  [3] annotate_1.42.0           AnnotationForge_1.6.1
>  [5] BatchJobs_1.2             BBmisc_1.6
>  [7] BiocParallel_0.6.1        biomaRt_2.20.0
>  [9] biovizBase_1.12.1         bit_1.1-12
> [11] bitops_1.0-6              brew_1.0-6
> [13] BSgenome_1.32.0           Category_2.30.0
> [15] cluster_1.15.2            codetools_0.2-8
> [17] colorspace_1.2-4          DESeq2_1.4.5
> [19] dichromat_2.0-0           digest_0.6.4
> [21] edgeR_3.6.2               evaluate_0.5.5
> [23] fail_1.2                  ff_2.2-13
> [25] foreach_1.4.2             formatR_0.10
> [27] Formula_1.1-1             genefilter_1.46.1
> [29] geneplotter_1.42.0        GenomicAlignments_1.0.1
> [31] GenomicFeatures_1.16.2    GenomicRanges_1.16.3
> [33] ggbio_1.12.4              ggplot2_1.0.0
> [35] GO.db_2.14.0              GOstats_2.30.0
> [37] graph_1.42.0              grid_3.1.0
> [39] gridExtra_0.9.1           GSEABase_1.26.0
> [41] gtable_0.1.2              Hmisc_3.14-4
> [43] hwriter_1.3               iterators_1.0.7
> [45] lattice_0.20-29           latticeExtra_0.6-26
> [47] locfit_1.5-9.1            MASS_7.3-33
> [49] Matrix_1.1-4              munsell_0.4.2
> [51] PFAM.db_2.14.0            plyr_1.8.1
> [53] preprocessCore_1.26.1     proto_0.3-10
> [55] R.methodsS3_1.6.1         R.oo_1.18.0
> [57] R.utils_1.32.4            RBGL_1.40.0
> [59] RColorBrewer_1.0-5        Rcpp_0.11.2
> [61] RcppArmadillo_0.4.300.8.0 RCurl_1.95-4.1
> [63] reshape2_1.4              Rsamtools_1.16.1
> [65] rtracklayer_1.24.2        scales_0.2.4
> [67] sendmailR_1.1-2           splines_3.1.0
> [69] stats4_3.1.0              stringr_0.6.2
> [71] survival_2.37-7           tools_3.1.0
> [73] VariantAnnotation_1.10.3  XML_3.98-1.1
> [75] xtable_1.7-3              zlibbioc_1.10.0
>
>
> Best
>
> Chao
>
>
>
>
>
>
>
>
>


-- 
Jason A. Hackney, Ph.D.
Bioinformatics and Computational Biology
Genentech
hackney.jason@gene.com
650-467-5084

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