MetagenomeSeq fitZig issue

[JingQiuyu]

when using fitZig function, after iteration, the stillActive=139, and the error message is as follows: Error in if (df2[1] > 1e+06) fit$F.p.value <- pchisq(df1 * fit$F, df1, : missing value where TRUE/FALSE needed

the fitting arguments are as follows: settings=zigControl(maxit=100,verbose=TRUE) fit=fitZig(obj=test_V,mod=mod,useCSSoffset = FALSE,control = settings)

Does anyone know what happened here?

[jnpaulson]

Do you have all zeros in a few of your samples?

On Thu, Jan 17, 2019 at 9:21 AM JingQiuyu notifications@github.com wrote:

when using fitZig function, after iteration, the stillActive=139, and the error message is as follows: Error in if (df2[1] > 1e+06) fit$F.p.value <- pchisq(df1 * fit$F, df1, : missing value where TRUE/FALSE needed

the fitting arguments are as follows: settings=zigControl(maxit=100,verbose=TRUE) fit=fitZig(obj=test_V,mod=mod,useCSSoffset = FALSE,control = settings)

Does anyone know what happened here?

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[JingQiuyu]

No, the count matrix is quite sparse. But for each sample, it's not all 0s.

[jnpaulson]

Feel free to email me an MRE and I’ll look into it. On Thu, Jan 17, 2019 at 10:02 AM JingQiuyu notifications@github.com wrote:

No, the count matrix is quite sparse. But for each sample, it's not all 0s.

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[JingQiuyu]

Hi Joseph,

It’s hard for me to send you the MRexperiment. The attached is the matrix after CSS normalization, with each column as one sample, and each row as one species. There are two groups of sample.

Looking forward to your opinion about the issue.

Best, Qiuyu

---

From: Joseph N. Paulson notifications@github.com Sent: Thursday, January 17, 2019 5:03:30 PM To: HCBravoLab/metagenomeSeq Cc: Qiuyu JING; Author Subject: Re: [HCBravoLab/metagenomeSeq] MetagenomeSeq fitZig issue (#64)

Feel free to email me an MRE and I’ll look into it. On Thu, Jan 17, 2019 at 10:02 AM JingQiuyu notifications@github.com wrote:

No, the count matrix is quite sparse. But for each sample, it's not all 0s.

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/HCBravoLab/metagenomeSeq/issues/64#issuecomment-455094371, or mute the thread https://github.com/notifications/unsubscribe-auth/AC5hg7gRqYQvH0R9iwTzhIfxZvtU6LBYks5vEDwhgaJpZM4aErXM .

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[eam12]

Was this error ever solved? I'm currently getting the same error.

[hcorrada]

Please post your sessionInfo()

[eam12]

sessionInfo()

R version 3.6.1 (2019-07-05) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages: [1] parallel stats graphics grDevices [5] utils datasets methods base

other attached packages: [1] dplyr_0.8.3 reshape2_1.4.3
[3] magrittr_1.5 phyloseq_1.28.0
[5] ggplot2_3.2.1 metagenomeSeq_1.26.2 [7] RColorBrewer_1.1-2 glmnet_2.0-18
[9] foreach_1.4.4 Matrix_1.2-17
[11] limma_3.40.5 Biobase_2.44.0
[13] BiocGenerics_0.30.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.1 locfit_1.5-9.1
[3] ape_5.3 lattice_0.20-38
[5] gtools_3.8.1 IHW_1.12.0
[7] Biostrings_2.52.0 digest_0.6.20
[9] assertthat_0.2.1 slam_0.1-45
[11] R6_2.4.0 plyr_1.8.4
[13] stats4_3.6.1 pillar_1.4.2
[15] gplots_3.0.1.1 zlibbioc_1.30.0
[17] rlang_0.4.0 lazyeval_0.2.2
[19] gdata_2.18.0 rstudioapi_0.10
[21] data.table_1.12.2 vegan_2.5-5
[23] S4Vectors_0.22.0 labeling_0.3
[25] splines_3.6.1 stringr_1.4.0
[27] igraph_1.2.4.1 Wrench_1.2.0
[29] munsell_0.5.0 compiler_3.6.1
[31] xfun_0.8 pkgconfig_2.0.2
[33] multtest_2.40.0 mgcv_1.8-28
[35] biomformat_1.12.0 tidyselect_0.2.5
[37] tibble_2.1.3 IRanges_2.18.1
[39] codetools_0.2-16 matrixStats_0.54.0 [41] permute_0.9-5 withr_2.1.2
[43] crayon_1.3.4 ggpubr_0.2.2
[45] bitops_1.0-6 MASS_7.3-51.4
[47] grid_3.6.1 nlme_3.1-140
[49] jsonlite_1.6 gtable_0.3.0
[51] scales_1.0.0 KernSmooth_2.23-15 [53] stringi_1.4.3 XVector_0.24.0
[55] ggsignif_0.6.0 fdrtool_1.2.15
[57] lpsymphony_1.12.0 Rhdf5lib_1.6.0
[59] iterators_1.0.12 tools_3.6.1
[61] ade4_1.7-13 glue_1.3.1
[63] purrr_0.3.2 survival_2.44-1.1 [65] colorspace_1.4-1 rhdf5_2.28.0
[67] cluster_2.1.0 caTools_1.17.1.2
[69] knitr_1.24

[hcorrada]

Thanks. Can you provide a reproducible example that raises this error?

[eam12]

We figured out the issue. Thank you!

[hcorrada]

Wonderful! Let us know if we can be of further help.