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JonathanRob / GeneSetAnalysisMatlab

Gene Set Analysis in Matlab (GSAM)
https://jonathanrob.github.io/GeneSetAnalysisMatlab-doc/
GNU General Public License v3.0
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error - loading .gmt #2

Closed intawat closed 1 year ago

intawat commented 1 year ago

Hi Jon,

I dowloaded the file HumanGEM_v1.12.0_symbols_metabolites.gmt and try to read into piano but it is not work as error when I want to se the object below

ERROR while rich displaying an object: Error in if (nchar(tmp[i]) > 15) tmp[i] <- paste(substr(tmp[i], 1, 15), : argument is of length zero

Traceback:

  1. tryCatch(withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler), error = outer_handler)
  2. tryCatchList(expr, classes, parentenv, handlers)
  3. tryCatchOne(expr, names, parentenv, handlers[[1L]])
  4. doTryCatch(return(expr), name, parentenv, handler)
  5. withCallingHandlers({ . if (!mime %in% names(repr::mime2repr)) . stop("No repr_* for mimetype ", mime, " in repr::mime2repr") . rpr <- repr::mime2repr[mime] . if (is.null(rpr)) . return(NULL) . prepare_content(is.raw(rpr), rpr) . }, error = error_handler)
  6. repr::mime2repr[mime]
  7. repr_text.default(obj)
  8. paste(capture.output(print(obj)), collapse = "\n")
  9. capture.output(print(obj))
  10. withVisible(...elt(i))
  11. print(obj)
  12. print.GSC(obj)
JonathanRob commented 1 year ago

Hi Intawat, it's hard to determine the cause from just the error message alone.

Could you include the commands that were run leading to the error?

intawat commented 1 year ago

It just simple as below. no error when loaded but when check the met object, the errors show. You mad a mouse version (from mouse GEM) for me months ago. It works very well.

met <- loadGSC('HumanGEM_v1.12.0_symbols_metabolites.gmt','gmt')

Best wishes, Intawat

On Tue, Sep 26, 2023 at 1:28 AM Jonathan Robinson @.***> wrote:

Hi Intawat, it's hard to determine the cause from just the error message alone.

Could you include the commands that were run leading to the error?

— Reply to this email directly, view it on GitHub https://github.com/JonathanRob/GeneSetAnalysisMatlab/issues/2#issuecomment-1734905673, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4VBHRCTQQBUYT2HB7FKM3X4JYXBANCNFSM6AAAAAA5GW2FMY . You are receiving this because you authored the thread.Message ID: @.***>

JonathanRob commented 1 year ago

Strange, I don't get the same error, and it seems to load fine. What version of Piano are you using? I used version 2.14.0 for my test.

intawat commented 1 year ago

No error when loaded

Please try to just execute the object that you created and enter then the error will show up. We can cannot use the object for genset calculation.

On Tue, Sep 26, 2023 at 7:48 AM Jonathan Robinson @.***> wrote:

Strange, I don't get the same error, and it seems to load fine. What version of Piano are you using? I used version 2.14.0 for my test.

— Reply to this email directly, view it on GitHub https://github.com/JonathanRob/GeneSetAnalysisMatlab/issues/2#issuecomment-1735477606, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4VBHTUZMBCTCQHTAKFAEDX4LFJ7ANCNFSM6AAAAAA5GW2FMY . You are receiving this because you authored the thread.Message ID: @.***>

JonathanRob commented 1 year ago

This is my exact input and output:

> library(piano)
> met <- loadGSC('HumanGEM_v1.12.0_symbols_metabolites.gmt', 'gmt')
> met
First 50 (out of 3656) gene set names:
 [1] "(+)-alpha-pinen..." "(-)-trans-carve..." "(10Z)-heptadece..." "(10Z)-heptadece..." "(11R)-HPETE"       
 [6] "(11Z)-docosenoy..." "(11Z)-eicosenoy..." "(11Z,14Z)-eicos..." "(11Z,14Z)-eicos..." "(11Z,14Z,17Z)-e..."
[11] "(11Z,14Z,17Z)-e..." "(11Z,14Z,17Z)-e..." "(13E)-11alpha-h..." "(13E)-tetranor-..." "(13E)-tetranor-..."
[16] "(13Z)-docosenoy..." "(13Z)-eicosenoi..." "(13Z)-eicosenoy..." "(13Z)-octadecen..." "(13Z)-octadecen..."
[21] "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(15Z)-tetracose..." "(15Z)-tetracose..."
[26] "(18E)-20-oxo-20..." "(18E)-20-oxo-20..." "(18R)-HEPE"         "(18R)-hydroxy-(..." "(1R)-hydroxy-(2..."
[31] "(1R,2S)-naphtha..." "(1S)-hydroxy-(2..." "(1S,2R)-naphtha..." "(1aalpha,2beta,..." "(24R)-24,25-dih..."
[36] "(24R,25R)3alpha..." "(24R,25R)3alpha..." "(2E)-Octadeceno..." "(2E)-decenoyl-C..." "(2E)-decenoyl-[..."
[41] "(2E)-docosenoyl..." "(2E)-dodecenoyl..." "(2E)-dodecenoyl..." "(2E)-eicosenoyl..." "(2E)-heneicosen..."
[46] "(2E)-heptadecen..." "(2E)-heptadecen..." "(2E)-heptenoyl-..." "(2E)-heptenoyl-..." "(2E)-hexacoseno..."

First 50 (out of 3060) gene names:
 [1] "CYP2C19" "CYP2C9"  "ABCA1"   "ACOT1"   "ACOT2"   "ACOT4"   "ACOT6"   "ACOT7"   "ACSBG1"  "ACSBG2"  "ACSL1"   "ACSL3"  
[13] "ACSL4"   "ACSL5"   "ACSL6"   "BAAT"    "CD36"    "CEL"     "FABP1"   "FABP12"  "FABP2"   "FABP3"   "FABP4"   "FABP5"  
[25] "FABP6"   "FABP7"   "FABP9"   "LIPA"    "MEIKIN"  "SLC27A1" "SLC27A2" "SLC27A3" "SLC27A4" "SLC27A6" "CPT1A"   "CPT1B"  
[37] "CPT1C"   "CPT2"    "CRAT"    "GPAM"    "GPAT2"   "GPAT3"   "GPAT4"   "SCD"     "SCD5"    "SOAT1"   "SOAT2"   "ALOX12" 
[49] "ACAA1"   "ACAA2"  

Gene set size summary:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
   1.00    2.00    5.00   11.57   11.00 1830.00 

First 10 gene sets with additional info:
      Gene set                  Additional info
 [1,] "(+)-alpha-pinene"        "na"           
 [2,] "(-)-trans-carveol"       "na"           
 [3,] "(10Z)-heptadecenoic ..." "na"           
 [4,] "(10Z)-heptadecenoyl-..." "na"           
 [5,] "(11R)-HPETE"             "na"           
 [6,] "(11Z)-docosenoyl-CoA"    "na"           
 [7,] "(11Z)-eicosenoyl-CoA"    "na"           
 [8,] "(11Z,14Z)-eicosadien..." "na"           
 [9,] "(11Z,14Z)-eicosadien..." "na"           
[10,] "(11Z,14Z,17Z)-eicosa..." "na"

Could you please check what version of Piano you are using, and/or try to re-download the .gmt file?

intawat commented 1 year ago

Thank you Jon, I use the same piano version. Sorry about this. Something wrong on my end. I will need to deeply investigate.

On Tue, Sep 26, 2023 at 8:53 AM Jonathan Robinson @.***> wrote:

This is my exact input and output:

library(piano) met <- loadGSC('HumanGEM_v1.12.0_symbols_metabolites.gmt', 'gmt') met First 50 (out of 3656) gene set names: [1] "(+)-alpha-pinen..." "(-)-trans-carve..." "(10Z)-heptadece..." "(10Z)-heptadece..." "(11R)-HPETE" [6] "(11Z)-docosenoy..." "(11Z)-eicosenoy..." "(11Z,14Z)-eicos..." "(11Z,14Z)-eicos..." "(11Z,14Z,17Z)-e..." [11] "(11Z,14Z,17Z)-e..." "(11Z,14Z,17Z)-e..." "(13E)-11alpha-h..." "(13E)-tetranor-..." "(13E)-tetranor-..." [16] "(13Z)-docosenoy..." "(13Z)-eicosenoi..." "(13Z)-eicosenoy..." "(13Z)-octadecen..." "(13Z)-octadecen..." [21] "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(15Z)-tetracose..." "(15Z)-tetracose..." [26] "(18E)-20-oxo-20..." "(18E)-20-oxo-20..." "(18R)-HEPE" "(18R)-hydroxy-(..." "(1R)-hydroxy-(2..." [31] "(1R,2S)-naphtha..." "(1S)-hydroxy-(2..." "(1S,2R)-naphtha..." "(1aalpha,2beta,..." "(24R)-24,25-dih..." [36] "(24R,25R)3alpha..." "(24R,25R)3alpha..." "(2E)-Octadeceno..." "(2E)-decenoyl-C..." "(2E)-decenoyl-[..." [41] "(2E)-docosenoyl..." "(2E)-dodecenoyl..." "(2E)-dodecenoyl..." "(2E)-eicosenoyl..." "(2E)-heneicosen..." [46] "(2E)-heptadecen..." "(2E)-heptadecen..." "(2E)-heptenoyl-..." "(2E)-heptenoyl-..." "(2E)-hexacoseno..."

First 50 (out of 3060) gene names: [1] "CYP2C19" "CYP2C9" "ABCA1" "ACOT1" "ACOT2" "ACOT4" "ACOT6" "ACOT7" "ACSBG1" "ACSBG2" "ACSL1" "ACSL3" [13] "ACSL4" "ACSL5" "ACSL6" "BAAT" "CD36" "CEL" "FABP1" "FABP12" "FABP2" "FABP3" "FABP4" "FABP5" [25] "FABP6" "FABP7" "FABP9" "LIPA" "MEIKIN" "SLC27A1" "SLC27A2" "SLC27A3" "SLC27A4" "SLC27A6" "CPT1A" "CPT1B" [37] "CPT1C" "CPT2" "CRAT" "GPAM" "GPAT2" "GPAT3" "GPAT4" "SCD" "SCD5" "SOAT1" "SOAT2" "ALOX12" [49] "ACAA1" "ACAA2"

Gene set size summary: Min. 1st Qu. Median Mean 3rd Qu. Max. 1.00 2.00 5.00 11.57 11.00 1830.00

First 10 gene sets with additional info: Gene set Additional info [1,] "(+)-alpha-pinene" "na" [2,] "(-)-trans-carveol" "na" [3,] "(10Z)-heptadecenoic ..." "na" [4,] "(10Z)-heptadecenoyl-..." "na" [5,] "(11R)-HPETE" "na" [6,] "(11Z)-docosenoyl-CoA" "na" [7,] "(11Z)-eicosenoyl-CoA" "na" [8,] "(11Z,14Z)-eicosadien..." "na" [9,] "(11Z,14Z)-eicosadien..." "na" [10,] "(11Z,14Z,17Z)-eicosa..." "na"

Could you please check what version of Piano you are using, and/or try to re-download the .gmt file?

— Reply to this email directly, view it on GitHub https://github.com/JonathanRob/GeneSetAnalysisMatlab/issues/2#issuecomment-1735589960, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4VBHRBLGX4M72MA6JG4C3X4LM57ANCNFSM6AAAAAA5GW2FMY . You are receiving this because you authored the thread.Message ID: @.***>

intawat commented 1 year ago

Found the problem is the download file from git was corrupted. It is strange that when I load the corrupted using the piano, it had no error. The problem fix by re download the file from th github and use the new one.

Sorry :)

//Intawat

On Tue, Sep 26, 2023 at 12:59 PM Intawat Nookaew @.***> wrote:

Thank you Jon, I use the same piano version. Sorry about this. Something wrong on my end. I will need to deeply investigate.

On Tue, Sep 26, 2023 at 8:53 AM Jonathan Robinson < @.***> wrote:

This is my exact input and output:

library(piano) met <- loadGSC('HumanGEM_v1.12.0_symbols_metabolites.gmt', 'gmt') met First 50 (out of 3656) gene set names: [1] "(+)-alpha-pinen..." "(-)-trans-carve..." "(10Z)-heptadece..." "(10Z)-heptadece..." "(11R)-HPETE" [6] "(11Z)-docosenoy..." "(11Z)-eicosenoy..." "(11Z,14Z)-eicos..." "(11Z,14Z)-eicos..." "(11Z,14Z,17Z)-e..." [11] "(11Z,14Z,17Z)-e..." "(11Z,14Z,17Z)-e..." "(13E)-11alpha-h..." "(13E)-tetranor-..." "(13E)-tetranor-..." [16] "(13Z)-docosenoy..." "(13Z)-eicosenoi..." "(13Z)-eicosenoy..." "(13Z)-octadecen..." "(13Z)-octadecen..." [21] "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(13Z,16Z)-docos..." "(15Z)-tetracose..." "(15Z)-tetracose..." [26] "(18E)-20-oxo-20..." "(18E)-20-oxo-20..." "(18R)-HEPE" "(18R)-hydroxy-(..." "(1R)-hydroxy-(2..." [31] "(1R,2S)-naphtha..." "(1S)-hydroxy-(2..." "(1S,2R)-naphtha..." "(1aalpha,2beta,..." "(24R)-24,25-dih..." [36] "(24R,25R)3alpha..." "(24R,25R)3alpha..." "(2E)-Octadeceno..." "(2E)-decenoyl-C..." "(2E)-decenoyl-[..." [41] "(2E)-docosenoyl..." "(2E)-dodecenoyl..." "(2E)-dodecenoyl..." "(2E)-eicosenoyl..." "(2E)-heneicosen..." [46] "(2E)-heptadecen..." "(2E)-heptadecen..." "(2E)-heptenoyl-..." "(2E)-heptenoyl-..." "(2E)-hexacoseno..."

First 50 (out of 3060) gene names: [1] "CYP2C19" "CYP2C9" "ABCA1" "ACOT1" "ACOT2" "ACOT4" "ACOT6" "ACOT7" "ACSBG1" "ACSBG2" "ACSL1" "ACSL3" [13] "ACSL4" "ACSL5" "ACSL6" "BAAT" "CD36" "CEL" "FABP1" "FABP12" "FABP2" "FABP3" "FABP4" "FABP5" [25] "FABP6" "FABP7" "FABP9" "LIPA" "MEIKIN" "SLC27A1" "SLC27A2" "SLC27A3" "SLC27A4" "SLC27A6" "CPT1A" "CPT1B" [37] "CPT1C" "CPT2" "CRAT" "GPAM" "GPAT2" "GPAT3" "GPAT4" "SCD" "SCD5" "SOAT1" "SOAT2" "ALOX12" [49] "ACAA1" "ACAA2"

Gene set size summary: Min. 1st Qu. Median Mean 3rd Qu. Max. 1.00 2.00 5.00 11.57 11.00 1830.00

First 10 gene sets with additional info: Gene set Additional info [1,] "(+)-alpha-pinene" "na" [2,] "(-)-trans-carveol" "na" [3,] "(10Z)-heptadecenoic ..." "na" [4,] "(10Z)-heptadecenoyl-..." "na" [5,] "(11R)-HPETE" "na" [6,] "(11Z)-docosenoyl-CoA" "na" [7,] "(11Z)-eicosenoyl-CoA" "na" [8,] "(11Z,14Z)-eicosadien..." "na" [9,] "(11Z,14Z)-eicosadien..." "na" [10,] "(11Z,14Z,17Z)-eicosa..." "na"

Could you please check what version of Piano you are using, and/or try to re-download the .gmt file?

— Reply to this email directly, view it on GitHub https://github.com/JonathanRob/GeneSetAnalysisMatlab/issues/2#issuecomment-1735589960, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4VBHRBLGX4M72MA6JG4C3X4LM57ANCNFSM6AAAAAA5GW2FMY . You are receiving this because you authored the thread.Message ID: @.***>

JonathanRob commented 1 year ago

Ah ok, good. No problem at all, I'm just glad we were able to solve the problem!