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: zoppo...@mail.nih.gov
________________________________________
From: Ted Harding [ted.hard...@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.
--------------------------------------------------------------------
E-Mail: (Ted Harding) <ted.hard...@manchester.ac.uk>
Fax-to-email: +44 (0)870 094 0861
Date: 23-May-10 Time: 23:31:25
------------------------------ XFMail ------------------------------
Cell A B Tissue
BR:BT_549 -3.80239 -0.43099 Breast
BR:HS578T -2.94118 1.1217 Breast
BR:MCF7 -4.00187 1.46303 Breast
BR:MDA_MB_231 -3.24907 1.58326 Breast
BR:T47D -3.41228 1.13818 Breast
CNS:SF_268 -3.63916 2.54378 CNS
CNS:SF_295 -3.09348 -1.00095 CNS
CNS:SF_539 -3.86184 1.39114 CNS
CNS:SNB_19 0.16583 0.03737 CNS
CNS:SNB_75 -0.23183 1.03945 CNS
CNS:U251 0.01263 1.66389 CNS
CO:HCT_116 -3.39764 0.43061 Colon
CO:COLO205 -3.64656 0.54344 Colon
CO:HCC_2998 -3.61457 -0.32362 Colon
CO:HCT_15 -3.45342 0.16357 Colon
CO:HT29 -4.11624 -0.02799 Colon
CO:KM12 -3.68703 2.19991 Colon
CO:SW_620 -1.53265 -1.35446 Colon
LC:A549 -2.66221 0.71215 Lung
LC:EKVX -4.32847 1.66042 Lung
LC:HOP_62 -3.4968 0.67884 Lung
LC:HOP_92 -3.60636 0.87116 Lung
LC:NCI_H226 -4.37408 -0.22311 Lung
LC:NCI_H23 -3.91625 -1.14955 Lung
LC:NCI_H322M -4.28534 1.66783 Lung
LC:NCI_H460 0.0042 -0.6023 Lung
LC:NCI_H522 -2.94381 0.3859 Lung
LE:CCRF_CEM -3.54526 -2.09262 Leukemia
LE:HL_60 -3.16745 -3.16745 Leukemia
LE:K_562 -0.58218 1.8581 Leukemia
LE:MOLT_4 -3.20055 -1.72841 Leukemia
LE:RPMI_8226 -2.59561 -1.9448 Leukemia
LE:SR -0.93541 2.95346 Leukemia
ME:LOXIMVI -4.2572 0.37259 Melanoma
ME:M14 -0.73942 -0.73904 Melanoma
ME:MALME_3M -0.67327 -1.33493 Melanoma
ME:MDA_MB_435 -0.1915 -0.16744 Melanoma
ME:MDA_N 0.21077 0.05502 Melanoma
ME:SK_MEL_2 0.55255 -1.6667 Melanoma
ME:SK_MEL_28 1.7425 1.45266 Melanoma
ME:SK_MEL_5 1.74749 -1.47817 Melanoma
ME:UACC_257 -0.72431 -1.84753 Melanoma
ME:UACC_62 0.52503 0.1605 Melanoma
OV:IGROV1 -4.02758 2.04324 Ovarian
OV:NCI_ADR_RES -3.04456 0.17046 Ovarian
OV:OVCAR_3 -3.0705 -0.31743 Ovarian
OV:OVCAR_4 -3.13137 -0.47497 Ovarian
OV:OVCAR_5 -3.7852 2.43038 Ovarian
OV:OVCAR_8 -3.66053 -0.9594 Ovarian
OV:SK_OV_3 -3.04477 2.15405 Ovarian
PR:DU_145 -4.33961 1.57548 Prostate
PR:PC_3 -3.36612 1.39328 Prostate
RE:786_0 -3.5086 1.75056 Renal
RE:A498 -2.89402 0.93287 Renal
RE:ACHN -3.96246 -0.62365 Renal
RE:CAKI_1 -2.48443 0.43245 Renal
RE:RXF_393 -3.49615 2.59144 Renal
RE:SN12C -3.90776 0.85244 Renal
RE:TK_10 -2.95281 1.26245 Renal
RE:UO_31 -3.99791 -1.09215 Renal
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