t.fit stops in masigpro while running RNA seq data
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subashika • 0
@2516a46c
Last seen 15 days ago
India

Hi

I have a problem in using the t.fit in the masigpro

below is my design file in dataframe ED

            Time replicates Control TMT_1 TMT_2.5 TMT_5

control_1week_1 7 1 1 0 0 0 control_1week_2 7 1 1 0 0 0 control_1week_4 7 1 1 0 0 0 control_24h_1 1 2 1 0 0 0 control_24h_3 1 2 1 0 0 0 control_24h_4 1 2 1 0 0 0 control_72h_1 3 3 1 0 0 0 control_72h_2 3 3 1 0 0 0 control_72h_3 3 3 1 0 0 0 TMT1_1week_1 7 4 0 1 0 0 TMT1_1week_2 7 4 0 1 0 0 TMT1_1week_3 7 4 0 1 0 0 TMT1_24h_1 1 5 0 1 0 0 TMT1_24h_2 1 5 0 1 0 0 TMT1_24h_3 1 5 0 1 0 0 TMT1_72h_1 3 6 0 1 0 0 TMT1_72h_2 3 6 0 1 0 0 TMT1_72h_3 3 6 0 1 0 0 TMT2.5_1week_2 7 7 0 0 1 0 TMT2.5_1week_3 7 7 0 0 1 0 TMT2.5_1week_4 7 7 0 0 1 0 TMT2.5_24h_1 1 8 0 0 1 0 TMT2.5_24h_2 1 8 0 0 1 0 TMT2.5_24h_3 1 8 0 0 1 0 TMT2.5_72h_2 3 9 0 0 1 0 TMT2.5_72h_3 3 9 0 0 1 0 TMT2.5_72h_4 3 9 0 0 1 0 TMT5_1week_1 7 10 0 0 0 1 TMT5_1week_3 7 10 0 0 0 1 TMT5_1week_4 7 10 0 0 0 1 TMT5_24h_1 1 11 0 0 0 1 TMT5_24h_2 1 11 0 0 0 1 TMT5_24h_4 1 11 0 0 0 1 TMT5_72h_1 3 12 0 0 0 1 TMT5_72h_2 3 12 0 0 0 1 TMT5_72h_4 3 12 0 0 0 1

I have a data file with 36 columns and 19,000 genes, every time i run t.fit it apruptly stops after fitting 2000 genes.

Is this happening because I have two many genes?



library(maSigPro) 

# load maSigPro library
# assigning experimntal design and 
>ED <- experimetnal.design_masigpro_tmt.second.run
>D <- `Processed_Data.(2)`


#making design

>design_D <- make.design.matrix(ED, degree = 2)

>design_D$groups.vector

# finding significant genes 

>fit_D <- p.vector(D, design_D, Q = 0.001, MT.adjust = "BH", min.obs = 20)

>fit_D$i # returns the number of significant genes
>fit_D$alfa # gives p-value at the Q false discovery control level, (I get NULL value here)
>fit_D$SELEC # is a matrix with the significant genes and their expression values (i get 8436 genes here)

#Finding significant differences

>tstep_D <- T.fit(fit_D, step.method = "backward", alfa = fit_D$Q, nvar.correction = TRUE)

#I also tried nvar correction to be false


########below is the error message I get 

[1] "fitting  gene 2000 out of 8436"
Error in if (fit$rank < nvars) coef[fit$pivot][seq.int(fit$rank + 1, nvars)] <- NA : 
  argument is of length zero
In addition: Warning messages:
1: In glm.fit(x = numeric(0), y = numeric(0), weights = NULL, start = NULL,  :
  no observations informative at iteration 1
2: glm.fit: algorithm did not converge 

sessionInfo( )

R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_India.1252  LC_CTYPE=English_India.1252   
[3] LC_MONETARY=English_India.1252 LC_NUMERIC=C                  
[5] LC_TIME=English_India.1252    

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

other attached packages:
[1] maSigPro_1.62.0

loaded via a namespace (and not attached):
[1] MASS_7.3-51.6       compiler_4.0.2      mclust_5.4.7        admisc_0.12        
[5] parallel_4.0.2      tools_4.0.2         Biobase_2.50.0      venn_1.10          
[9] BiocGenerics_0.36.1
RNASeqData maSigPro • 52 views
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please lemme know if I am not communicating my problem clearly. I am new to forums like this.

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