[R] "order" issue

Zoppoli, Gabriele (NIH/NCI) [G] zoppolig at mail.nih.gov
Mon May 24 00:43:30 CEST 2010


crazy stuff!!! I tried to reload the txt file, and now it's working...

this is the original (attached)

thanks!

Gabriele Zoppoli, MD
Ph.D. Fellow, Experimental and Clinical Oncology and Hematology, University of Genova, Genova, Italy
Guest Researcher, LMP, NCI, NIH, Bethesda MD

Work: 301-451-8575
Mobile: 301-204-5642
Email: zoppolig at mail.nih.gov
________________________________________
From: Ted Harding [Ted.Harding at manchester.ac.uk]
Sent: Sunday, May 23, 2010 6:31 PM
To: Zoppoli, Gabriele (NIH/NCI) [G]
Cc: R help
Subject: RE: [R] "order" issue

On 23-May-10 21:39:06, Zoppoli, Gabriele (NIH/NCI) [G] wrote:
> Hi everybody, this is a real dummy thing.
>
> I sorted a matrix based on a given column, and what I get is right,
> until it comes to columns of negative and positive values; than,
> "order" orders everything from max to min in the negative values, and
> then AGAIN from max to min in the positive values!!!
>
> Why isn't everything order from max to min, and that's it?
> Thank you!!!
>
> Attached is the txt file I use; try:
>
> x=x[order(x[,2]),]
>
> What I get is:
>
> print(x)
>
>           Product A B   Tissue
> 44  ME:MDA_MB_435     -0.1915    -0.16744 Melanoma
> 17     CNS:SNB_75    -0.23183     1.03945      CNS
> 37       LE:K_562    -0.58218      1.8581 Leukemia
> 43    ME:MALME_3M    -0.67327    -1.33493 Melanoma
> 49    ME:UACC_257    -0.72431    -1.84753 Melanoma
> 42         ME:M14    -0.73942    -0.73904 Melanoma
> 40          LE:SR    -0.93541     2.95346 Leukemia
> 25      CO:SW_620    -1.53265    -1.35446    Colon
> 63      RE:CAKI_1    -2.48443     0.43245    Renal
> 39   LE:RPMI_8226    -2.59561     -1.9448 Leukemia
> 26        LC:A549    -2.66221     0.71215     Lung
> 61        RE:A498    -2.89402     0.93287    Renal
> 9       BR:HS578T    -2.94118      1.1217   Breast
> 34    LC:NCI_H522    -2.94381      0.3859     Lung
> 66       RE:TK_10    -2.95281     1.26245    Renal
> 52 OV:NCI_ADR_RES    -3.04456     0.17046  Ovarian
> 57     OV:SK_OV_3    -3.04477     2.15405  Ovarian
> 53     OV:OVCAR_3     -3.0705    -0.31743  Ovarian
> 14     CNS:SF_295    -3.09348    -1.00095      CNS
> 54     OV:OVCAR_4    -3.13137    -0.47497  Ovarian
> 36       LE:HL_60    -3.16745    -3.16745 Leukemia
> 38      LE:MOLT_4    -3.20055    -1.72841 Leukemia
> 11  BR:MDA_MB_231    -3.24907     1.58326   Breast
> 59        PR:PC_3    -3.36612     1.39328 Prostate
> 19     CO:HCT_116    -3.39764     0.43061    Colon
> 12        BR:T47D    -3.41228     1.13818   Breast
> 22      CO:HCT_15    -3.45342     0.16357    Colon
> 64     RE:RXF_393    -3.49615     2.59144    Renal
> 28      LC:HOP_62     -3.4968     0.67884     Lung
> 60       RE:786_0     -3.5086     1.75056    Renal
> 35    LE:CCRF_CEM    -3.54526    -2.09262 Leukemia
> 29      LC:HOP_92    -3.60636     0.87116     Lung
> 21    CO:HCC_2998    -3.61457    -0.32362    Colon
> 13     CNS:SF_268    -3.63916     2.54378      CNS
> 20     CO:COLO205    -3.64656     0.54344    Colon
> 56     OV:OVCAR_8    -3.66053     -0.9594  Ovarian
> 24        CO:KM12    -3.68703     2.19991    Colon
> 55     OV:OVCAR_5     -3.7852     2.43038  Ovarian
> 8       BR:BT_549    -3.80239    -0.43099   Breast
> 15     CNS:SF_539    -3.86184     1.39114      CNS
> 65       RE:SN12C    -3.90776     0.85244    Renal
> 31     LC:NCI_H23    -3.91625    -1.14955     Lung
> 62        RE:ACHN    -3.96246    -0.62365    Renal
> 67       RE:UO_31    -3.99791    -1.09215    Renal
> 10        BR:MCF7    -4.00187     1.46303   Breast
> 51      OV:IGROV1    -4.02758     2.04324  Ovarian
> 23        CO:HT29    -4.11624    -0.02799    Colon
> 41     ME:LOXIMVI     -4.2572     0.37259 Melanoma
> 32   LC:NCI_H322M    -4.28534     1.66783     Lung
> 27        LC:EKVX    -4.32847     1.66042     Lung
> 58      PR:DU_145    -4.33961     1.57548 Prostate
> 30    LC:NCI_H226    -4.37408    -0.22311     Lung
> 33    LC:NCI_H460      0.0042     -0.6023     Lung
> 18       CNS:U251     0.01263     1.66389      CNS
> 16     CNS:SNB_19     0.16583     0.03737      CNS
> 45       ME:MDA_N     0.21077     0.05502 Melanoma
> 50     ME:UACC_62     0.52503      0.1605 Melanoma
> 46    ME:SK_MEL_2     0.55255     -1.6667 Melanoma
> 47   ME:SK_MEL_28      1.7425     1.45266 Melanoma
> 48    ME:SK_MEL_5     1.74749    -1.47817 Melanoma
>
> Gabriele Zoppoli, MD

Somewhat strange indeed! The only further question I can think of
is to ask how what did "x" look like before your re-ordered it.
Using the "x.txt" file you supplied, I get:

  x <- read.table("x.txt")
  str(x)
  # 'data.frame':   60 obs. of  4 variables:
  #  $ Product: Factor w/ 60 levels "BR:BT_549","BR:HS578T",..: 37 10 30
  #    36 42 35 33 18 56 32 ...
  #  $ A      : num  -0.192 -0.232 -0.582 -0.673 -0.724 ...
  #  $ B      : num  -0.167 1.039 1.858 -1.335 -1.848 ...
  #  $ Tissue : Factor w/ 9 levels "Breast","CNS",..: 6 2 4 6 6 6 4 3 9 4
  #    ...


so x[,2] and x[,3] are indeed numeric. Then (similar to yours):

  X<-x[order(x[,2]),]
  print(X)
  #           Product        A        B   Tissue
  # 30    LC:NCI_H226 -4.37408 -0.22311     Lung
  # 58      PR:DU_145 -4.33961  1.57548 Prostate
  # 27        LC:EKVX -4.32847  1.66042     Lung
  # 32   LC:NCI_H322M -4.28534  1.66783     Lung
  # 41     ME:LOXIMVI -4.25720  0.37259 Melanoma
  # 23        CO:HT29 -4.11624 -0.02799    Colon
  # 51      OV:IGROV1 -4.02758  2.04324  Ovarian
  # 10        BR:MCF7 -4.00187  1.46303   Breast
  # 67       RE:UO_31 -3.99791 -1.09215    Renal
  # 62        RE:ACHN -3.96246 -0.62365    Renal
  # 31     LC:NCI_H23 -3.91625 -1.14955     Lung
  # 65       RE:SN12C -3.90776  0.85244    Renal
  # 15     CNS:SF_539 -3.86184  1.39114      CNS
  # 8       BR:BT_549 -3.80239 -0.43099   Breast
  # 55     OV:OVCAR_5 -3.78520  2.43038  Ovarian
  # 24        CO:KM12 -3.68703  2.19991    Colon
  # 56     OV:OVCAR_8 -3.66053 -0.95940  Ovarian
  # 20     CO:COLO205 -3.64656  0.54344    Colon
  # 13     CNS:SF_268 -3.63916  2.54378      CNS
  # 21    CO:HCC_2998 -3.61457 -0.32362    Colon
  # 29      LC:HOP_92 -3.60636  0.87116     Lung
  # 35    LE:CCRF_CEM -3.54526 -2.09262 Leukemia
  # 60       RE:786_0 -3.50860  1.75056    Renal
  # 28      LC:HOP_62 -3.49680  0.67884     Lung
  # 64     RE:RXF_393 -3.49615  2.59144    Renal
  # 22      CO:HCT_15 -3.45342  0.16357    Colon
  # 12        BR:T47D -3.41228  1.13818   Breast
  # 19     CO:HCT_116 -3.39764  0.43061    Colon
  # 59        PR:PC_3 -3.36612  1.39328 Prostate
  # 11  BR:MDA_MB_231 -3.24907  1.58326   Breast
  # 38      LE:MOLT_4 -3.20055 -1.72841 Leukemia
  # 36       LE:HL_60 -3.16745 -3.16745 Leukemia
  # 54     OV:OVCAR_4 -3.13137 -0.47497  Ovarian
  # 14     CNS:SF_295 -3.09348 -1.00095      CNS
  # 53     OV:OVCAR_3 -3.07050 -0.31743  Ovarian
  # 57     OV:SK_OV_3 -3.04477  2.15405  Ovarian
  # 52 OV:NCI_ADR_RES -3.04456  0.17046  Ovarian
  # 66       RE:TK_10 -2.95281  1.26245    Renal
  # 34    LC:NCI_H522 -2.94381  0.38590     Lung
  # 9       BR:HS578T -2.94118  1.12170   Breast
  # 61        RE:A498 -2.89402  0.93287    Renal
  # 26        LC:A549 -2.66221  0.71215     Lung
  # 39   LE:RPMI_8226 -2.59561 -1.94480 Leukemia
  # 63      RE:CAKI_1 -2.48443  0.43245    Renal
  # 25      CO:SW_620 -1.53265 -1.35446    Colon
  # 40          LE:SR -0.93541  2.95346 Leukemia
  # 42         ME:M14 -0.73942 -0.73904 Melanoma
  # 49    ME:UACC_257 -0.72431 -1.84753 Melanoma
  # 43    ME:MALME_3M -0.67327 -1.33493 Melanoma
  # 37       LE:K_562 -0.58218  1.85810 Leukemia
  # 17     CNS:SNB_75 -0.23183  1.03945      CNS
  # 44  ME:MDA_MB_435 -0.19150 -0.16744 Melanoma
  # 33    LC:NCI_H460  0.00420 -0.60230     Lung
  # 18       CNS:U251  0.01263  1.66389      CNS
  # 16     CNS:SNB_19  0.16583  0.03737      CNS
  # 45       ME:MDA_N  0.21077  0.05502 Melanoma
  # 50     ME:UACC_62  0.52503  0.16050 Melanoma
  # 46    ME:SK_MEL_2  0.55255 -1.66670 Melanoma
  # 47   ME:SK_MEL_28  1.74250  1.45266 Melanoma
  # 48    ME:SK_MEL_5  1.74749 -1.47817 Melanoma

and now the values in X[,2] are indeed in the correct numerical order,
yet essentially the same command as your has been executed.

I have not succeeded in repoducing your result by ordering on other
columns of "x" or on the row-names of "x".

So it is a mystery! The only thing I can think of is that the
columns of "x" (as seen by R) are different from what you think
they should be. Since your file "x.txt" looks like the value
of "x" after your re-ordering, it is impossible to test such
guesses on the original "x".

Ted.


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Date: 23-May-10                                       Time: 23:31:25
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