[R] "order" issue
David Winsemius
dwinsemius at comcast.net
Mon May 24 00:52:48 CEST 2010
On May 23, 2010, at 6:32 PM, Zoppoli, Gabriele (NIH/NCI) [G] wrote:
> This is what I get:
>
> str(x)
>
> chr [1:60, 1:4] "ME:SK_MEL_5" "ME:SK_MEL_28" "ME:SK_MEL_2" ...
> - attr(*, "dimnames")=List of 2
> ..$ : chr [1:60] "48" "47" "46" "50" ...
> ..$ : chr [1:4] "Product" "hsa.miR.204" "hsa.miR.210" "Tissue"
>
> It doesn't make much sense to me...
How did you bring that text file into R? Both Ted and I are getting:
> 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 ...
Your "x" is a 60 x 4 matrix of all character elements.
If I try:
x[ order(as.character(x[,2])),]
I get the same behavior as you describe.
--
David.
>
> I would like to have the second column ordered from max to min, or
> from min to max (with the argument decreasing=TRUE), but "order"
> seems to reorder everything without considering negative number as
> smaller than positive ones...
>
>
> 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: Jim Holtman [jholtman at gmail.com]
> Sent: Sunday, May 23, 2010 6:07 PM
> To: Zoppoli, Gabriele (NIH/NCI) [G]
> Cc: R help
> Subject: Re: [R] "order" issue
>
> do 'str' on your object to see if you have factors where you think you
> have numerics.
>
> What is the problem you are trying to solve?
>
> Sent from my iPhone.
>
> On May 23, 2010, at 17:39, "Zoppoli, Gabriele (NIH/NCI) [G]" <zoppolig at mail.nih.gov
>> 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
>> 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
>> <x.txt>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
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