[BioC] cellHTS Repeat Values in Text Output

[Joseph Barry]

Dear Mark,

getTopTable() has not been dealing properly with multi-channel data. Clearly it should, in order to be useful for cases such as yours. I have therefore now updated the function accordingly, and you can find it in cellHTS2 devel (2.25.3). You can see from the example below that it now outputs the replicate and channel information from the raw and summarized data correctly.

Being able to have a separate score per channel is a feature that is potentially generally useful for users. Let me discuss this with the others and get back to you.

I would generally advise against manually setting the state vector, but sometimes performing your own normalization or summarization is necessary so if you know what you are doing it is fine.

# load example data
library(cellHTS2)
data(KcViabSmall)
x <- KcViabSmall

# simulate data for two channels
ch1 <- matrix(runif(2*1152), 1152, 2, dimnames=list(1:1152,1:2))
ch2 <- matrix(runif(2*1152), 1152, 2, dimnames=list(1:1152,1:2))
assayData(x) <- do.call(assayDataNew,list(ch1=ch1,ch2=ch2))

# an example normalization
xn <- normalizePlates(x, scale="multiplicative", method="median", 
                      varianceAdjust="none")
xsc <- scoreReplicates(xn, sign="-", method="zscore") 
xsc <- summarizeReplicates(xsc, "mean")
xsc <- summarizeChannels(xsc, fun=function(r1,r2) r1+r2)

# getTopTable output
tab <- getTopTable(cellHTSlist=list("raw"=x,"normalized"=xn, "scored"=xsc), file="testtable.txt")
head(tab)

Thanks again for your feedback! Please do keep us updated on any additional issues.

Best wishes,
Joe

On May 23, 2013, at 7:14 AM, Mark Dane wrote:

> Hi,
> 
> I am seeing a problem with the text output in my multi-channel experiment. I have different types of data so I want to normalize and score the channels separately. Therefore, I do not want to run summarizeReplicates. I think the following will show what I am doing:
> 
> x <- readPlateList("Platelist.txt", name=experimentName, path=dataPath)
> x <- configure(x, "Description.txt", "Plateconf.txt", "Screenlog.txt",
>               path=dataPath) 
> xn <- normalizePlates(x, scale="multiplicative", method="median", 
>                      varianceAdjust="none")
> xsc <- scoreReplicates(xn, sign="-", method="zscore") 
> xsc at state[3]=TRUE
> getTopTable(cellHTSlist=list("raw"=x,"normalized"=xn, "scored"=xsc),
>            file="testtable.txt")
> 
> The output in testtable.txt (and similarly in writeReport's text output) has repeated values that are not what is actually in the cellHTS objects.
> 
> raw'G01plate	position	well	score	wellAnno	finalWellAnno	raw_r1_ch1	raw_r2_ch1	raw_r1_ch2	raw_r2_ch2	median_ch1	diff_ch1	median_ch2	diff_ch2	raw/PlateMedian_r1_ch1	raw/PlateMedian_r2_ch1	raw/PlateMedian_r1_ch2	raw/PlateMedian_r2_ch2	normalized_r1_ch1	normalized_r2_ch1	normalized_r1_ch2	normalized_r2_ch2
> 3	145	G01	3.33	sample	sample	80	80	80	80	80	0	80	0	0.0502	0.0502	0.0502	0.0502	0.05	0.05	0.05	0.05
> 1	7	A07	3.33	sample	sample	80	80	80	80	80	0	80	0	0.051	0.051	0.051	0.051	0.051	0.051	0.051	0.051
> 3	202	I10	3.27	sample	sample	110	110	110	110	110	0	110	0	0.069	0.069	0.069	0.069	0.069	0.069	0.069	0.069
> 
> Is it ok to force the scored state of xsc to TRUE? Please let me know if I'm using this correctly. I really appreciate your prior quick and helpful responses.
> 
> thank you,
> 
> Mark Dane
> Computational Biology Master Student
> Oregon Health and Science University
> 
> 
> 
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] grid      parallel  stats     graphics  grDevices utils     datasets  methods  
> [9] base     
> 
> other attached packages:
> [1] lattice_0.20-15    gdata_2.12.0.2     cellHTS2_2.25.1    locfit_1.5-9.1    
> [5] hwriter_1.3        vsn_3.29.0         splots_1.27.0      genefilter_1.43.0 
> [9] Biobase_2.21.2     BiocGenerics_0.7.2 RColorBrewer_1.0-5 spade_1.9.0       
> [13] igraph0_0.5.7     
> 
> loaded via a namespace (and not attached):
> [1] affy_1.39.2           affyio_1.29.0         annotate_1.39.0      
> [4] AnnotationDbi_1.23.11 BiocInstaller_1.11.1  Category_2.27.1      
> [7] DBI_0.2-7             feature_1.2.8         flowCore_1.27.15     
> [10] graph_1.39.0          GSEABase_1.23.0       gtools_2.7.1         
> [13] IRanges_1.19.8        ks_1.8.12             limma_3.17.12        
> [16] MASS_7.3-26           prada_1.37.0          preprocessCore_1.23.0
> [19] RBGL_1.37.2           robustbase_0.9-7      rrcov_1.3-3          
> [22] RSQLite_0.11.3        splines_3.0.0         stats4_3.0.0         
> [25] survival_2.37-4       tools_3.0.0           XML_3.95-0.2         
> [28] xtable_1.7-1          zlibbioc_1.7.0   
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