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I get this error running the following command on a gene expression data frame of dimensions 395x99, the problem is It runs fine when applied to smaller data frames (395x81). I have seen the error comes from when a function is recursive. But I don't see that here or why It works depending on the dimensions.

normalized <-  raw  %>% column_to_rownames("Gene") %>%
  filter_at(.,vars(contains(colnames(raw))),any_vars(. !=0)) %>%
  filter_at(.,vars(contains(colnames(raw))),any_vars(. > 10)) %>%
  mutate(media=dplyr::select(.,contains(colnames(raw))) %>% rowMeans) %>%
  filter(media>10) %>% dplyr::select(-media) %>%  as.matrix %>%
  varianceStabilizingTransformation() %>% as.data.frame %>% 
  mutate(variance=apply(.,1,var)) 

dput(head(raw))
structure(list(Gene = structure(c(330L, 246L, 97L, 125L, 7L, 
16L), .Label = c("ABCF1", "ADGRE5", "ADORA2A", "AIF1", "AKT1", 
"ALOX15B", "ARG1", "AXL", "B3GAT1", "BAGE", "BATF", "BCL2", "BCL2L11", 
"BCL6", "BRCA1", "BRCA2", "BST2", "BTLA", "BUB1", "C10orf54", 
"C1QA", "C1QB", "CA4", "CBLB", "CCL17", "CCL18", "CCL2", "CCL20", 
"CCL21", "CCL22", "CCL3", "CCL4", "CCL5", "CCNB2", "CCR1", "CCR2", 
"CCR4", "CCR5", "CCR6", "CCR7", "CD14", "CD160", "CD163", "CD19", 
"CD1C", "CD1D", "CD2", "CD209", "CD22", "CD226", "CD244", "CD247", 
"CD27", "CD274", "CD276", "CD28", "CD33", "CD37", "CD38", "CD3D", 
"CD3E", "CD3G", "CD4", "CD40", "CD40LG", "CD44", "CD47", "CD48", 
"CD52", "CD53", "CD6", "CD63", "CD68", "CD69", "CD70", "CD74", 
"CD79A", "CD79B", "CD80", "CD83", "CD86", "CD8A", "CD8B", "CDK1", 
"CDKN2A", "CDKN3", "CEACAM1", "CEACAM8", "CIITA", "CLEC4C", "CMKLR1", 
"CORO1A", "CRTAM", "CSF1R", "CSF2RB", "CTAG1B", "CTAG2", "CTLA4", 
"CTSS", "CX3CL1", "CX3CR1", "CXCL1", "CXCL10", "CXCL11", "CXCL13", 
"CXCL8", "CXCL9", "CXCR2", "CXCR3", "CXCR4", "CXCR5", "CXCR6", 
"CYBB", "DDX58", "DGAT2", "DMBT1", "EBI3", "EFNA4", "EGFR", "EGR2", 
"EGR3", "EIF2AK2", "ENTPD1", "EOMES", "FAS", "FASLG", "FCER1G", 
"FCGR1A", "FCGR2B", "FCGR3A", "FCGR3B", "FCRLA", "FOXM1", "FOXO1", 
"FOXP3", "FUT4", "FYB", "G6PD", "GADD45GIP1", "GAGE1,GAGE12I,GAGE12F", 
"GAGE10", "GAGE12J", "GAGE13", "GAGE2C,GAGE2A,GAGE2E", "GATA3", 
"GBP1", "GNLY", "GPR18", "GRAP2", "GUSB", "GZMA", "GZMB", "GZMH", 
"GZMK", "HAVCR2", "HERC6", "HGF", "HIF1A", "HLA-A", "HLA-B", 
"HLA-C", "HLA-DMA", "HLA-DMB", "HLA-DOA", "HLA-DOB", "HLA-DPA1", 
"HLA-DPB1", "HLA-DQA1", "HLA-DQA2", "HLA-DQB2", "HLA-DRA", "HLA-DRB1", 
"HLA-E", "HLA-F", "HLA-F-AS1", "HLA-G", "HMBS", "ICAM1", "ICOS", 
"ICOSLG", "ID2", "ID3", "IDO1", "IDO2", "IFI27", "IFI35", "IFI44L", 
"IFI6", "IFIH1", "IFIT1", "IFIT2", "IFIT3", "IFITM1", "IFITM2", 
"IFNA17", "IFNB1", "IFNG", "IGF1R", "IGSF6", "IKZF1", "IKZF2", 
"IKZF3", "IKZF4", "IL10", "IL10RA", "IL12A", "IL12B", "IL13", 
"IL15", "IL17A", "IL17F", "IL18", "IL1A", "IL1B", "IL2", "IL21", 
"IL22", "IL23A", "IL2RA", "IL2RB", "IL2RG", "IL3RA", "IL4", "IL6", 
"IL7", "IL7R", "IRF1", "IRF4", "IRF9", "IRS1", "ISG15", "ISG20", 
"ITGA1", "ITGAE", "ITGAL", "ITGAM", "ITGAX", "ITGB1", "ITGB2", 
"ITGB7", "ITK", "JAML", "JCHAIN", "KIAA0101", "KIR2DL1", "KIR2DL2", 
"KIR2DL3", "KLF2", "KLRB1", "KLRD1", "KLRF1", "KLRG1", "KLRK1", 
"KREMEN1", "KRT5", "KRT7", "LAG3", "LAMP1", "LAMP3", "LAPTM5", 
"LCK", "LCN2", "LEXM", "LILRB1", "LILRB2", "LMNA", "LRG1", "LRP1", 
"LST1", "LY9", "LYZ", "M6PR", "MAD2L1", "MADCAM1", "MAGEA1", 
"MAGEA10", "MAGEA12", "MAGEA3", "MAGEA4", "MAGEC2", "MAPK1", 
"MAPK14", "MELK", "MIF", "MKI67", "MLANA", "MMP2", "MMP9", "MPO", 
"MRC1", "MS4A1", "MTOR", "MX1", "MYC", "NCAM1", "NCF1", "NCR1", 
"NCR3", "NECTIN2", "NFATC1", "NFKBIA", "NKG7", "NOS2", "NOTCH3", 
"NRP1", "NT5E", "NTN3", "OAS1", "OAS2", "OAS3", "PDCD1", "PDCD1LG2", 
"PECAM1", "PGF", "PIK3CA", "PIK3CD", "PMEL", "POLR2A", "POU2AF1", 
"PRDM1", "PRF1", "PSMB9", "PTEN", "PTGS2", "PTK7", "PTPN11", 
"PTPN6", "PTPN7", "PTPRC", "PTPRCAP", "PVR", "PYGL", "RB1", "RORC", 
"RPS6", "S100A8", "S100A9", "SAMHD1", "SDHA", "SELL", "SH2D1A", 
"SH2D1B", "SIT1", "SKAP2", "SLAMF7", "SLAMF8", "SNAI1", "SNAI2", 
"SRGN", "SSX2", "STAT1", "STAT3", "STAT4", "STAT5A", "STAT6", 
"TAGAP", "TAP1", "TARP", "TBP", "TBX21", "TCF7", "TDO2", "TFRC", 
"TGFB1", "TIGIT", "TLR3", "TLR7", "TLR8", "TLR9", "TNF", "TNFAIP8", 
"TNFRSF14", "TNFRSF17", "TNFRSF18", "TNFRSF4", "TNFRSF9", "TNFSF10", 
"TNFSF13B", "TNFSF14", "TNFSF18", "TNFSF4", "TNFSF9", "TOP2A", 
"TP63", "TRIM29", "TUBB", "TWIST1", "TYROBP", "VCAM1", "VEGFA", 
"VTCN1", "XAGE1B", "ZAP70", "ZBTB46", "ZEB1"), class = "factor"), 
    `21` = c(217L, 6L, 44L, 5008L, 4L, 646L), `98` = c(69L, 7L, 
    0L, 2121L, 430L, 880L), `100` = c(32L, 0L, 0L, 1128L, 106L, 
    1869L), `101` = c(35L, 0L, 2L, 957L, 26L, 783L), `102` = c(63L, 
    5L, 0L, 3759L, 21L, 270L), `103` = c(26L, 11L, 0L, 2553L, 
    332L, 279L), `104` = c(51L, 1L, 0L, 983L, 84L, 307L), `105` = c(70L, 
    1L, 0L, 1800L, 7L, 767L), `107` = c(57L, 1L, 0L, 4698L, 0L, 
    1165L), `109` = c(81L, 5L, 0L, 2727L, 26L, 131L), `112` = c(162L, 
    0L, 0L, 3663L, 1L, 598L), `113` = c(32L, 0L, 318L, 795L, 
    43L, 1019L), `114` = c(23L, 0L, 0L, 1147L, 10L, 835L), `115` = c(198L, 
    10L, 0L, 3375L, 1L, 578L), `116` = c(89L, 1L, 0L, 2623L, 
    3L, 1267L), `118` = c(105L, 0L, 68L, 5056L, 3L, 405L), `119` = c(21L, 
    0L, 0L, 1691L, 0L, 223L), `120` = c(36L, 0L, 6L, 2834L, 0L, 
    1240L), `121` = c(221L, 21L, 0L, 3587L, 34L, 775L), `122` = c(132L, 
    0L, 0L, 2439L, 30L, 222L), `123` = c(112L, 3L, 826L, 3488L, 
    25L, 200L), `124` = c(43L, 0L, 82L, 2959L, 3L, 514L), `126` = c(21L, 
    0L, 0L, 1220L, 24L, 789L), `127` = c(48L, 3L, 13L, 2065L, 
    1L, 179L), `128` = c(117L, 0L, 0L, 2415L, 4L, 355L), `129` = c(99L, 
    1L, 32L, 1849L, 2L, 411L), `131` = c(61L, 3L, 0L, 1331L, 
    5L, 1688L), `132` = c(49L, 1L, 0L, 1089L, 21L, 886L), `133` = c(28L, 
    0L, 42L, 1444L, 3L, 446L), `134` = c(91L, 1L, 15L, 1067L, 
    29L, 1097L), `135` = c(102L, 0L, 72L, 1293L, 5L, 255L), `136` = c(40L, 
    6L, 0L, 1339L, 2L, 115L), `137` = c(93L, 0L, 111L, 1934L, 
    4L, 231L), `138` = c(10L, 0L, 13L, 1341L, 136L, 416L), `139` = c(123L, 
    0L, 583L, 3135L, 1L, 361L), `140` = c(28L, 0L, 11L, 2439L, 
    7L, 495L), `141` = c(39L, 0L, 59L, 1623L, 2L, 441L), `143` = c(28L, 
    0L, 1266L, 1190L, 0L, 607L), `144` = c(20L, 0L, 30L, 794L, 
    4L, 869L), `145` = c(11L, 3L, 1L, 1145L, 1L, 203L), `146` = c(128L, 
    0L, 1833L, 1462L, 1L, 2050L), `147` = c(77L, 4L, 15L, 2733L, 
    3L, 234L), `148` = c(23L, 0L, 0L, 1122L, 1L, 182L), `149` = c(14L, 
    0L, 0L, 520L, 5L, 766L), `150` = c(180L, 0L, 12L, 2595L, 
    0L, 321L), `151` = c(64L, 4L, 0L, 2868L, 11L, 476L), `152` = c(107L, 
    0L, 6L, 2268L, 6L, 955L), `153` = c(50L, 1L, 198L, 1763L, 
    16L, 319L), `156` = c(57L, 1L, 129L, 2856L, 5L, 312L), `157` = c(27L, 
    0L, 5L, 3122L, 0L, 276L), `158` = c(45L, 4L, 0L, 2696L, 2L, 
    824L), `159` = c(121L, 0L, 0L, 1338L, 4L, 622L), `161` = c(154L, 
    0L, 1L, 3090L, 0L, 1004L), `162` = c(35L, 0L, 0L, 1683L, 
    2L, 260L), `164` = c(29L, 0L, 24L, 847L, 43L, 767L), `165` = c(37L, 
    0L, 8L, 712L, 2L, 1062L), `166` = c(18L, 0L, 450L, 805L, 
    88L, 125L), `167` = c(59L, 0L, 0L, 1871L, 3L, 456L), `169` = c(107L, 
    5L, 0L, 1702L, 0L, 337L), `170` = c(104L, 0L, 1241L, 1610L, 
    5L, 183L), `172` = c(34L, 0L, 19L, 812L, 2L, 834L), `174` = c(19L, 
    0L, 0L, 2559L, 0L, 1019L), `175` = c(109L, 0L, 633L, 5560L, 
    0L, 204L), `176` = c(83L, 0L, 794L, 2534L, 0L, 391L), `178` = c(39L, 
    2L, 0L, 1973L, 2L, 352L), `179` = c(61L, 0L, 0L, 3200L, 2L, 
    2257L), `180` = c(17L, 0L, 6L, 261L, 50L, 101L), `181` = c(9L, 
    0L, 157L, 285L, 1L, 1780L), `182` = c(92L, 0L, 6L, 1670L, 
    0L, 874L), `185` = c(32L, 5L, 1L, 1182L, 1L, 437L), `187` = c(51L, 
    0L, 0L, 2337L, 4L, 108L), `188` = c(101L, 0L, 0L, 2979L, 
    30L, 351L), `189` = c(285L, 2L, 0L, 2150L, 0L, 303L), `190` = c(113L, 
    0L, 0L, 12932L, 18L, 400L), `191` = c(94L, 1L, 0L, 1683L, 
    2L, 197L), `193` = c(353L, 0L, 0L, 2401L, 12L, 393L), `195` = c(86L, 
    1L, 2497L, 1845L, 9L, 614L), `196` = c(42L, 0L, 76L, 1703L, 
    4L, 159L), `197` = c(12L, 4L, 1L, 499L, 3L, 627L), `198` = c(68L, 
    0L, 1L, 2301L, 0L, 219L), `199` = c(89L, 4L, 0L, 2845L, 5L, 
    339L), `200` = c(30L, 0L, 0L, 1316L, 89L, 299L), `201` = c(33L, 
    4L, 0L, 1860L, 0L, 259L), `202` = c(35L, 4L, 0L, 6607L, 3L, 
    306L), `204` = c(10L, 1L, 1L, 498L, 3L, 440L), `206` = c(89L, 
    6L, 0L, 3961L, 9L, 256L), `207` = c(78L, 4L, 3L, 2203L, 24L, 
    129L), `208` = c(77L, 7L, 1399L, 1499L, 0L, 446L), `209` = c(42L, 
    1L, 2440L, 1677L, 1L, 60L), `210` = c(56L, 1L, 0L, 1716L, 
    39L, 610L), `212` = c(89L, 6L, 29L, 2736L, 5L, 976L), `213` = c(128L, 
    2L, 1L, 1624L, 4L, 523L), `214` = c(49L, 0L, 0L, 1360L, 112L, 
    1787L), `216` = c(44L, 0L, 0L, 1392L, 110L, 2026L), `219` = c(64L, 
    2L, 39L, 2733L, 57L, 316L), `220` = c(105L, 0L, 1L, 2491L, 
    27L, 417L), `222` = c(11L, 12L, 0L, 1073L, 64L, 374L), `247` = c(77L, 
    0L, 0L, 2115L, 37L, 558L)), row.names = c(NA, 6L), class = "data.frame")

I have tried changing the stack size as described here but still no luck

Jose Gracia Rodriguez
  • 167
  • 8
  • Could you provide some example data? E.g. by using `dput(head(raw))` – Dominik Rafacz Jul 04 '22 at 08:35
  • Sure!, no problem – Jose Gracia Rodriguez Jul 04 '22 at 08:52
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    The short answer to your question would be: you are using `filter_at` inappropriately. And I am not sure what you are trying to achieve. I'm assuming that you want to retain only genes in which any of the values in a row is unequal to zero... but this is not the way. You should call `filter(if_any(everything(), ~ . != 0))` in this case. If you want to do something else -- you need to expain what you want. I don't even understand the structure of your data. BTW -- `filter_at` is superseded by `filter(across())`, what you can see in my suggestion. – Dominik Rafacz Jul 04 '22 at 09:01

0 Answers0