Entering edit mode
Abhishek Pratap
▴
160
@abhishek-pratap-6167
Last seen 10.3 years ago
Hi Michael and Simon
I am starting to use DESeq2 on a 60 sample count data and seeing it
report
NA p-values for multiple genes. Not sure if this is due to cooks
distance
or some other thing. I did see the seqanswer thread to turn off cooks
distance but dint work for me in DESeq2
Copying just one example.. unfortunately the formatting will be messed
up.
Let me know if there is a good place to copy it for easier reading.
Thanks!
-Abhi
baseMean log2FoldChange lfcSE stat pvalue
padj
SYMBOL
16012 58 5.556873e+01 1.4310814 0.2586475 5.532941 NA
NA
mcols(diff_exp_result)[16012,]
DataFrame with 1 row and 23 columns
baseMean baseVar allZero dispGeneEst dispGeneEstConv dispFit
dispersion dispIter dispConv dispOutlier dispMAP Intercept
<numeric> <numeric> <logical> <numeric> <logical> <numeric>
<numeric> <numeric> <logical> <logical> <numeric> <numeric>
1 1.437498 3.786966 FALSE 1.302189 TRUE 1.987536
1.404384 8 TRUE FALSE 1.404384 0.2919642
condition_high_vs_low SE_Intercept SE_condition_high_vs_low
WaldStatistic_Intercept WaldStatistic_condition_high_vs_low
<numeric> <numeric> <numeric>
<numeric> <numeric>
1 0.3913094 0.3133799 0.2582543
0.9316622 1.51521
WaldPvalue_Intercept WaldPvalue_condition_high_vs_low betaConv
betaIter
deviance maxCooks
<numeric> <numeric> <logical>
<numeric>
<numeric> <numeric>
1 0.3515111 0.1297193 TRUE
6
184.0293 0.5676499
> sessionInfo()
R version 3.0.1 (2013-05-16)
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] parallel stats graphics grDevices utils datasets
methods
base
other attached packages:
[1] synapseClient_0.32-1 getopt_1.20.0
TxDb.Hsapiens.UCSC.hg19.knownGene_2.10.1
[4] GenomicFeatures_1.14.0 GGally_0.4.4
pheatmap_0.7.7
[7] gplots_2.12.1 RColorBrewer_1.0-5
Rsamtools_1.14.1
[10] Biostrings_2.30.1 gdata_2.13.2
reshape_0.8.4
[13] plyr_1.8 ggplot2_0.9.3.1
DESeq2_1.2.5
[16] RcppArmadillo_0.3.920.1 Rcpp_0.10.6
GenomicRanges_1.14.3
[19] XVector_0.2.0 IRanges_1.20.5
org.Hs.eg.db_2.10.1
[22] RSQLite_0.11.4 DBI_0.2-7
AnnotationDbi_1.24.0
[25] Biobase_2.22.0 BiocGenerics_0.8.0
BiocInstaller_1.12.0
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