(rnaseq) [yangxm@sonmi 5.deg]$ Rscript $scriptdir/deseq_analysis.r -i $workdir/4.expression/all_gene_count.tsv -g normal_vs_tumor.compare.txt  -k $workdir/4.expression/all_gene_fpkm.tsv -r normal --fdr 1 --fc 1.1 -p normal_vs_tumor

Loading required package: ggplot2

Loading required package: edgeR

Loading required package: limma

[1] "abstract_factors is start"

[1] "abstract_factors is over"

[1] "read count data ..."

[1] "read count data is over"

[1] "fpkm data ..."

[1] "fpkm data is over"

[1] "normal" "normal" "normal" "tumor"  "tumor"  "tumor" 

[1] "do std_two_condition_comp start ..."

Loading required package: S4Vectors

Loading required package: stats4

Loading required package: BiocGenerics

Attaching package: ‘BiocGenerics’

The following object is masked from ‘package:limma’:

    plotMA

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,

    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,

    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,

    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,

    Position, rank, rbind, Reduce, rownames, sapply, saveRDS, setdiff,

    table, tapply, union, unique, unsplit, which.max, which.min

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:utils’:

    findMatches

The following objects are masked from ‘package:base’:

    expand.grid, I, unname

Loading required package: IRanges

Loading required package: GenomicRanges

Loading required package: GenomeInfoDb

Loading required package: SummarizedExperiment

Loading required package: MatrixGenerics

Loading required package: matrixStats

Attaching package: ‘MatrixGenerics’

The following objects are masked from ‘package:matrixStats’:

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,

    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,

    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,

    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,

    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,

    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,

    colWeightedMeans, colWeightedMedians, colWeightedSds,

    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,

    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,

    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,

    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,

    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,

    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,

    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,

    rowWeightedSds, rowWeightedVars

Loading required package: Biobase

Welcome to Bioconductor

    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.

Attaching package: ‘Biobase’

The following object is masked from ‘package:MatrixGenerics’:

    rowMedians

The following objects are masked from ‘package:matrixStats’:

    anyMissing, rowMedians

Attaching package: ‘DESeq2’

The following object is masked _by_ ‘.GlobalEnv’:

    fpkm

[1] "normal" "normal" "normal" "tumor"  "tumor"  "tumor" 

[1] normal normal normal tumor  tumor  tumor 

Levels: normal tumor

                normal_rep1 normal_rep2 normal_rep3 tumor_rep1 tumor_rep2

ENSG00000008735           0           0           0          0          0

ENSG00000015475          30          37          37         41         47

ENSG00000025708          25          26          19         32         18

ENSG00000025770         106          99         111        265        303

ENSG00000040608           0           0           0          0          0

ENSG00000054611           2           1           3          0          0

                tumor_rep3

ENSG00000008735          0

ENSG00000015475         45

ENSG00000025708         24

ENSG00000025770        263

ENSG00000040608          0

ENSG00000054611          0

                normal_rep1 normal_rep2 normal_rep3 tumor_rep1 tumor_rep2

ENSG00000008735           0           0           0          0          0

ENSG00000015475          30          37          37         41         47

ENSG00000025708          25          26          19         32         18

ENSG00000025770         106          99         111        265        303

ENSG00000040608           0           0           0          0          0

ENSG00000054611           2           1           3          0          0

                tumor_rep3

ENSG00000008735          0

ENSG00000015475         45

ENSG00000025708         24

ENSG00000025770        263

ENSG00000040608          0

ENSG00000054611          0

                normal_rep1 normal_rep2 normal_rep3 tumor_rep1 tumor_rep2

ENSG00000008735      0.0000     0.00000     0.00000      0.000     0.0000

ENSG00000015475   1327.7438  1623.03374  1613.84909   1474.461  1654.6048

ENSG00000025708   1347.2917  1388.76181  1009.12134   1401.290   771.6094

ENSG00000025770   3507.6257  3246.94822  3619.91623   7125.406  7975.4168

ENSG00000040608      0.0000     0.00000     0.00000      0.000     0.0000

ENSG00000054611     56.1383    27.82031    82.98864      0.000     0.0000

                tumor_rep3

ENSG00000008735      0.000

ENSG00000015475   1574.790

ENSG00000025708   1022.704

ENSG00000025770   6881.455

ENSG00000040608      0.000

ENSG00000054611      0.000

                normal_rep1 normal_rep2 normal_rep3 tumor_rep1 tumor_rep2

ENSG00000015475  1327.74383  1623.03374  1613.84909  1474.4608  1654.6048

ENSG00000025708  1347.29171  1388.76181  1009.12134  1401.2898   771.6094

ENSG00000025770  3507.62571  3246.94822  3619.91623  7125.4057  7975.4168

ENSG00000054611    56.13830    27.82031    82.98864     0.0000     0.0000

ENSG00000070010   394.52809   543.09802   453.62072   445.2478   435.8618

ENSG00000073150    36.18087     0.00000    71.31440     0.0000     0.0000

                tumor_rep3

ENSG00000015475  1574.7902

ENSG00000025708  1022.7042

ENSG00000025770  6881.4551

ENSG00000054611     0.0000

ENSG00000070010   485.2668

ENSG00000073150     0.0000

[1] "create DEG_list object is over"

[1] "the number of origin gene is 1082"

[1] "the number of gene (after filtering) is 425"

 

Warning: The system is configured to read the RTC time in the local time zone.

         This mode cannot be fully supported. It will create various problems

         with time zone changes and daylight saving time adjustments. The RTC

         time is never updated, it relies on external facilities to maintain it.

         If at all possible, use RTC in UTC by calling

         'timedatectl set-local-rtc 0'.

estimating size factors

estimating dispersions

gene-wise dispersion estimates

mean-dispersion relationship

-- note: fitType='parametric', but the dispersion trend was not well captured by the

   function: y = a/x + b, and a local regression fit was automatically substituted.

   specify fitType='local' or 'mean' to avoid this message next time.

final dispersion estimates

fitting model and testing

[1] "------------------------------res-----------------------------------------\n"

log2 fold change (MLE): condition tumor vs normal 

Wald test p-value: condition tumor vs normal 

DataFrame with 6 rows and 6 columns

                  baseMean log2FoldChange     lfcSE      stat      pvalue

                 <numeric>      <numeric> <numeric> <numeric>   <numeric>

ENSG00000015475  39.044620      0.1533438  0.243529  0.629675 5.28907e-01

ENSG00000025708  23.964443     -0.1221735  0.319085 -0.382887 7.01803e-01

ENSG00000025770 184.845181      1.1922151  0.132801  8.977478 2.77043e-19

ENSG00000054611   1.067586     -3.6443993  2.173883 -1.676447 9.36506e-02

ENSG00000070010  23.431703      0.0841112  0.314202  0.267698 7.88932e-01

ENSG00000073150   0.533206     -2.6428859  3.994739 -0.661592 5.08233e-01

                       padj

                  <numeric>

ENSG00000015475 6.80968e-01

ENSG00000025708 8.15375e-01

ENSG00000025770 1.20524e-17

ENSG00000054611 1.80863e-01

ENSG00000070010 8.70643e-01

ENSG00000073150          NA

[1] 0.1375035

[1] "aaaaaaaaaaaaaaaaa\n"

[1] "bb\n"

[1] "hello"

[1] 286

[1] "logical"

[1] "do std_two_condition_comp start is over"

Warning messages:

1: `qplot()` was deprecated in ggplot2 3.4.0. 

2: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.

ℹ Please use `linewidth` instead. 

3: In DESeqDataSet(se, design = design, ignoreRank) :

  some variables in design formula are characters, converting to factors

4: Removed 116 rows containing missing values or values outside the scale range (`geom_point()`). 

5: Removed 116 rows containing missing values or values outside the scale range (`geom_point()`). 

(rnaseq) [yangxm@sonmi 5.deg]$ ls

normal_vs_tumor.all.tsv      normal_vs_tumor.cor.png        normal_vs_tumor.FC_count.png

normal_vs_tumor.compare.txt  normal_vs_tumor.DEG.final.tsv  normal_vs_tumor.FC_FDR.pdf

normal_vs_tumor.cor.pdf      normal_vs_tumor.FC_count.pdf   normal_vs_tumor.FC_FDR.png