Hello!

I have some RNA-seq data from a mixture of cell types and I am using CAMTHC to see if I can possibly deconvolute the data and then compare it to a similar treated mixture. In the Vignette it suggests normalized counts and so I figured that RPKM from edgeR would be best. I filtered out all of the zero expression rows and additionally chopped out rows that were poorly annotated and low expression.

I am trying to run CAMTHC on the control samples first, and then the treatment. Here is what the data.frame looks like.

> head(data1)
                     S2_RPKM   S4_RPKM
ENSRNOG00000000007  1.320103  4.150496
ENSRNOG00000000008  3.148846  1.958280
ENSRNOG00000000010 36.373405 28.564685
ENSRNOG00000000017 16.856564 32.637097
ENSRNOG00000000024  1.847236  1.237173
ENSRNOG00000000033  8.120219  4.865989
> str(data1)
 num [1:14330, 1:2] 1.32 3.15 36.37 16.86 1.85 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:14330] "ENSRNOG00000000007" "ENSRNOG00000000008" "ENSRNOG00000000010" "ENSRNOG00000000017" ...
  ..$ : chr [1:2] "S2_RPKM" "S4_RPKM"

I would expect that there would be about 15 to 16 cell types in this tissue. So when I run through the example code in the Vignette I get this:

> library(CAMTHC)
> set.seed(111)
> rCAM <- CAM(data1, K = 2:5, thres.low = 0.30, thres.high = 0.95)
Preprocessing

Registered S3 method overwritten by 'xts':
  method     from
  as.zoo.xts zoo 
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 
outlier cluster number: 2

convex hull cluster number: 2

Marker Gene Selection

A and S Matrix Estimation

Warning message:
In FUN(...) : Return NULL for K = 5 larger than 2
Warning message:
In FUN(...) : Return NULL for K = 3 larger than 2
Warning message:
In FUN(...) : Return NULL for K = 4 larger than 2
Warning message:
Quick-TRANSfer stage steps exceeded maximum (= 454600)

I get this 'Quick-TRANSfer' error, which I have no idea about. The plot ifrom "plot(MDL(rCAM), data.term = TRUE)" is blank.

When I look at the output of CAM it looks like this:

> str(rCAM)
    Formal class 'CAMObj' [package "CAMTHC"] with 3 slots
      ..@ PrepResult :Formal class 'CAMPrepObj' [package "CAMTHC"] with 8 slots
      .. .. ..@ Valid    : Named logi [1:14275] FALSE FALSE TRUE TRUE FALSE TRUE ...
      .. .. .. ..- attr(*, "names")= chr [1:14275] "ENSRNOG00000000007" "ENSRNOG00000000008" "ENSRNOG00000000010" "ENSRNOG00000000017" ...
      .. .. ..@ Xprep    : num [1:2, 1:9092] 45.92 -5.52 35 11.16 9.18 ...
      .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. ..$ : chr [1:2] "P1" ""
      .. .. .. .. ..$ : chr [1:9092] "ENSRNOG00000000010" "ENSRNOG00000000017" "ENSRNOG00000000033" "ENSRNOG00000000034" ...
      .. .. ..@ Xproj    : num [1:2, 1:9092] 1 -0.12 1 0.319 1 ...
      .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. ..$ : chr [1:2] "P1" ""
      .. .. .. .. ..$ : chr [1:9092] "ENSRNOG00000000010" "ENSRNOG00000000017" "ENSRNOG00000000033" "ENSRNOG00000000034" ...
      .. .. ..@ W        : num [1:2, 1:2] 0.707 -0.707 0.707 0.707
      .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. ..$ : chr [1:2] "P1" ""
      .. .. .. .. ..$ : NULL
      .. .. ..@ SW       : num [1:2] 1 1
      .. .. ..@ cluster  :List of 2
      .. .. .. ..$ cluster: Named int [1:9092] 18 4 22 37 46 17 31 5 4 23 ...
      .. .. .. .. ..- attr(*, "names")= chr [1:9092] "ENSRNOG00000000010" "ENSRNOG00000000017" "ENSRNOG00000000033" "ENSRNOG00000000034" ...
      .. .. .. ..$ size   : int [1:50] 314 167 172 145 163 392 135 107 136 64 ...
      .. .. ..@ c.outlier: int [1:2] 20 24
      .. .. ..@ centers  : num [1:2, 1:2] 1 -0.874 1 0.472
      .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. ..$ : chr [1:2] "" "medcenters"
      .. .. .. .. ..$ : chr [1:2] "12" "25"
      ..@ MGResult   :List of 4
      .. ..$ 2:Formal class 'CAMMGObj' [package "CAMTHC"] with 3 slots
      .. .. .. ..@ idx   : num [1:2] 1 1
      .. .. .. ..@ corner: int [1:2, 1:2] 12 12 25 25
      .. .. .. ..@ error : num[0 , 0 ] 
      .. ..$ 3: NULL
      .. ..$ 4: NULL
      .. ..$ 5: NULL
      ..@ ASestResult:List of 4
      .. ..$ 2:Formal class 'CAMASObj' [package "CAMTHC"] with 10 slots
      .. .. .. ..@ Aest      : num [1:2, 1:2] 0.6575 0.0442 0.3425 0.9558
      .. .. .. ..@ Sest      : num [1:14275, 1:2] 0 3.81 40.73 8.04 2.19 ...
      .. .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. .. ..$ : chr [1:14275] "ENSRNOG00000000007" "ENSRNOG00000000008" "ENSRNOG00000000010" "ENSRNOG00000000017" ...
      .. .. .. .. .. ..$ : NULL
      .. .. .. ..@ Aest.proj : num [1:2, 1:2] 1.3251 0.0891 0.3731 1.0411
      .. .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. .. ..$ : NULL
      .. .. .. .. .. ..$ : chr [1:2] "12" "25"
      .. .. .. ..@ Ascale    : num [1:2] 0.496 0.918
      .. .. .. ..@ AestO     : num [1:2, 1:2] 0.6575 0.0442 0.3425 0.9558
      .. .. .. ..@ SestO     : num [1:14275, 1:2] 0 3.81 40.73 8.04 2.19 ...
      .. .. .. .. ..- attr(*, "dimnames")=List of 2
      .. .. .. .. .. ..$ : chr [1:14275] "ENSRNOG00000000007" "ENSRNOG00000000008" "ENSRNOG00000000010" "ENSRNOG00000000017" ...
      .. .. .. .. .. ..$ : NULL
      .. .. .. ..@ AestO.proj: num [1:2, 1:2] 0.937 0.063 0.264 0.736
      .. .. .. ..@ AscaleO   : num [1:2] 0.702 1.298
      .. .. .. ..@ datalength: num [1:3] -64280 -64280 -64280
      .. .. .. ..@ mdl       : num [1:3] -57983 -57983 -57983
      .. ..$ 3: NULL
      .. ..$ 4: NULL
      .. ..$ 5: NULL

Any advice or feedback is greatly appreciated. TIA

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE Leap 15.0

Matrix products: default
BLAS/LAPACK: /usr/local/lib/OpenBLAS_home/lib/libopenblas_zenp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8          LC_NUMERIC=C                 
 [3] LC_TIME=en_US.UTF-8           LC_COLLATE=en_US.UTF-8       
 [5] LC_MONETARY=en_US.UTF-8       LC_MESSAGES=en_US.UTF-8      
 [7] LC_PAPER=en_US.UTF-8          LC_NAME=en_US.UTF-8          
 [9] LC_ADDRESS=en_US.UTF-8        LC_TELEPHONE=en_US.UTF-8     
[11] LC_MEASUREMENT=en_US.UTF-8    LC_IDENTIFICATION=en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] CAMTHC_1.2.0        Biobase_2.44.0      BiocGenerics_0.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.2          mvtnorm_1.0-11      lattice_0.20-38    
 [4] corpcor_1.6.9       class_7.3-15        zoo_1.8-6          
 [7] gtools_3.8.1        assertthat_0.2.1    digest_0.6.22      
[10] foreach_1.4.7       gridBase_0.4-7      R6_2.4.0           
[13] plyr_1.8.4          DMwR_0.4.1          magic_1.5-9        
[16] pcaPP_1.9-73        ggplot2_3.2.1       pillar_1.4.2       
[19] gplots_3.0.1.1      rlang_0.4.1         lazyeval_0.2.2     
[22] curl_4.2            gdata_2.18.0        TTR_0.23-5         
[25] rpart_4.1-15        BiocParallel_1.18.1 stringr_1.4.0      
[28] munsell_0.5.0       compiler_3.6.1      pkgconfig_2.0.3    
[31] pkgmaker_0.27       tidyselect_0.2.5    tibble_2.1.3       
[34] codetools_0.2-16    crayon_1.3.4        dplyr_0.8.3        
[37] withr_2.1.2         bitops_1.0-6        grid_3.6.1         
[40] xtable_1.8-4        gtable_0.3.0        registry_0.5-1     
[43] magrittr_1.5        scales_1.0.0        bibtex_0.4.2       
[46] KernSmooth_2.23-16  quantmod_0.4-15     stringi_1.4.3      
[49] ROCR_1.0-7          reshape2_1.4.3      doParallel_1.0.15  
[52] geometry_0.4.4      xts_0.11-2          RColorBrewer_1.1-2 
[55] NMF_0.21.0          iterators_1.0.12    tools_3.6.1        
[58] glue_1.3.1          purrr_0.3.3         rngtools_1.4       
[61] abind_1.4-5         colorspace_1.4-1    cluster_2.1.0      
[64] caTools_1.17.1.2    rJava_0.9-11