Dear BioC list,

After searching the BioC list and books and googling, I still cannot figure
out the questions which are described below. Any suggestions will be really
appreciated.

1. I have wt, mut-a, mut-b strains, each of them has 2 replicates. After
implementation of heatmap_2 function in Heatplus package, I got result and
understand how the dendrogram is generated, but I am confused that how to
interpret the color assigned to each of the genes. Supposed gene-x is red(
fold-change : -2), what it is relative to? to wt or to overall samples?

2. I tried to use altcdfenv package to only get the S. cerevisiae
environment, however, I always got error in the first step to wrap the
environment: "Error in validObject(.Object) :  invalid class "CdfEnvAffy"
object: invalid object for slot "envir" in class "CdfEnvAffy": got class
"CdfEnvAffy", should be or extend class "environment".

My abatch@cdfName is "Yeast_2" and annotation file is yeast2. Or if there is
any alternative way to filter out S. pombe signals??
By the way, there are lots of cdf files about yeast2, which one is the most
updated?


Thank you in advance!!
Hui-Yi



R version 2.6.2 (2008-02-08)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

attached base packages:
 [1] tcltk     splines   tools     stats     graphics  grDevices utils
datasets
 [9] methods   base

other attached packages:
 [1] org.Sc.sgd.db_2.0.2  altcdfenvs_1.12.0    makecdfenv_1.16.0
 [4] yeast2.db_2.0.2      affycoretools_1.10.2 annaffy_1.10.1
 [7] KEGG_2.0.1           GO_2.0.1             biomaRt_1.12.2
[10] RCurl_0.8-1          GOstats_2.4.0        Category_2.4.0
[13] RBGL_1.16.0          GO.db_2.0.2          graph_1.18.0
[16] siggenes_1.12.0      yeast2_2.0.1         Heatplus_1.8.0
[19] RColorBrewer_1.0-2   yeast2cdf_2.0.0      limma_2.12.0
[22] geneplotter_1.16.0   lattice_0.17-10      annotate_1.16.1
[25] xtable_1.5-2         AnnotationDbi_1.0.6  RSQLite_0.6-9
[28] DBI_0.2-4            multtest_1.18.0      simpleaffy_2.14.05
[31] genefilter_1.16.0    survival_2.34-1      affyPLM_1.14.0
[34] gcrma_2.10.0         matchprobes_1.10.0   affy_1.16.0
[37] preprocessCore_1.0.0 affyio_1.6.1         Biobase_1.16.3

loaded via a namespace (and not attached):
[1] cluster_1.11.11    grid_2.6.2         KernSmooth_2.22-22 XML_1.93-2.1

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