Re: [R] need help for t.test using by
any one 1Rnwb wrote: I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)). when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) Error in t.test.formula(IL1Ra ~ Group, data = .sub) : grouping factor must have exactly 2 levels I checked my data file and the plate ID has P16-P47 and the disease column is Y/N. I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong. for more detail i amm posting a part of my data. SampleID PlateID Sex Disease DurationAge prt1prt2 prt3prt4 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 10P16 M N 0.916030215 242.3011559 36.40117263 90.135962.08 11P16 F Y 14975.2542.08281552 133.8052501 29.0570764 260.55 1280.29 12P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 13P16 F Y 292225.08300169 231.6043765 9.022844487 902.53 37571.39 14P16 F Y 12053.2537.49924765 158.6370595 24.90606549 1.63471.15 15P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 16P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 17P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 18P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 19P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 20P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 21P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 22P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 23P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 24P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 25P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 26P17 M Y 12053.2550.91548265 173.7764722 18.90280088 52.25 15962.05 27P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 28P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 29P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 30P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 31P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 32P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 33P17 M Y 876631.74913978 220.2561296 34.40329218 130.31 2377.36 34P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 35P17 M Y 12053.2536.1661567 212.1613578 96.51775947 621.42 3269.9 36P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 37P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 38P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58 39P18 F N 14.2496731
Re: [R] need help for t.test using by
On Aug 19, 2009, at 9:00 AM, 1Rnwb wrote: any one I looked at your posting yesterday and could not figure out what your statistical question was, nor could I figure out how the t.test formula related to the column names in the data.frame. I saw no Group or IL1Ra variables in your data. I also tried to import that data and found that you had more column headers than columns. I gave up. -- DW 1Rnwb wrote: I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)). when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) Error in t.test.formula(IL1Ra ~ Group, data = .sub) : grouping factor must have exactly 2 levels I checked my data file and the plate ID has P16-P47 and the disease column is Y/N. I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong. for more detail i amm posting a part of my data. SampleIDPlateID Sex Disease DurationAge prt1prt2 prt3prt4 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 10 P16 M N 0.916030215 242.3011559 36.40117263 90.135962.08 11 P16 F Y 14975.2542.08281552 133.8052501 29.0570764 260.55 1280.29 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 13 P16 F Y 292225.08300169 231.6043765 9.022844487 902.53 37571.39 14 P16 F Y 12053.2537.49924765 158.6370595 24.90606549 1.63471.15 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 26 P17 M Y 12053.25 50.91548265 173.7764722 18.90280088 52.25 15962.05 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 33 P17 M Y 876631.74913978 220.2561296 34.40329218 130.31 2377.36 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 35 P17 M Y 12053.2536.1661567 212.1613578 96.51775947 621.42 3269.9 36 P17 M Y 8035.5 57.91540599 115.2852178
Re: [R] need help for t.test using by
Thanks for the reply, and sorry for not being clear, I have ELISA data for 50 plates, equal number of disease and control samples are located on each plates. I need to do the ttest between each proteins listed as prt1, prt2... prt50 on all the plates 1-50, however for some proteins i have data for 40 plates and that is creating the problem for me when I run by(eo,eo$PlateID, function(.sub) t.test(prt1~Disease,data=.sub)). If i only take the data for 40 plates, this command works, unfortunately I do not want to make multiple copies of the same data over to do things. Similarlyby(eo,eo$sex,function(.sub) t.test(prt1~Disease,data=.sub)) is also not working when I select the data for 40 plates. I used these two formulas earlier sucessfully. I am uploading a part of data as a delim file for sample http://www.nabble.com/file/p25051220/r..txt r..txt . Thanks 1Rnwb wrote: any one 1Rnwb wrote: I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)). when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) Error in t.test.formula(IL1Ra ~ Group, data = .sub) : grouping factor must have exactly 2 levels I checked my data file and the plate ID has P16-P47 and the disease column is Y/N. I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong. for more detail i amm posting a part of my data. SampleID PlateID Sex Disease DurationAge prt1prt2 prt3prt4 1P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 2P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 3P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 4P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 5P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 6P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 7P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 8P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 9P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 10 P16 M N 0.916030215 242.3011559 36.40117263 90.135962.08 11 P16 F Y 14975.2542.08281552 133.8052501 29.0570764 260.55 1280.29 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 13 P16 F Y 292225.08300169 231.6043765 9.022844487 902.53 37571.39 14 P16 F Y 12053.2537.49924765 158.6370595 24.90606549 1.63471.15 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 26 P17 M Y 12053.2550.91548265 173.7764722 18.90280088 52.25 15962.05 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 31 P17 M Y 16071 54.49906148
[R] need help for t.test using by
I am trying to do ttest for each plate which has equal number of disease and controls. by searching this forum I found one posting suggesting OP to use by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)). when i modified this for my use I used to get the pvalues for each plate, recently upgraded to R2.9.x and now i am getting following error when i use this by(eo,PlateID, function(.sub) t.test(IL1Ra~Group,data=.sub)) Error in t.test.formula(IL1Ra ~ Group, data = .sub) : grouping factor must have exactly 2 levels I checked my data file and the plate ID has P16-P47 and the disease column is Y/N. I have search all but could not locate the answer. Can anyone suggest me the direction where i am going wrong. for more detail i amm posting a part of my data. SampleIDPlateID Sex Disease DurationAge prt1prt2 prt3prt4 1 P16 F N 25.33282811 836.08979 20.04582692 295.74 11731.43 2 P16 F N 32.74912883 243.0652116 53.16487056 383.63 4451.36 3 P16 M N 3.49961999 181.5587298 23.24604762 522.52 325.52 4 P16 M N 5.249771666 261.0978097 19.69024684 833.61 2229.04 5 P16 M N 39.16612385 237.334794 83.97284692 694.03 1204.36 6 P16 F N 33.49929145 540.486536 29.69569346 895.36 72105.75 7 P16 F N 3.915997361 5215.378446 35.44324704 1023.63 101680.69 8 P16 F N 33.49929145 466.5188732 12.93422535 814.26 7169.61 9 P16 F N 38.1661348 706.5117791 19.69024684 331.62 7296.72 10 P16 M N 0.916030215 242.3011559 36.40117263 90.135962.08 11 P16 F Y 14975.2542.08281552 133.8052501 29.0570764 260.55 1280.29 12 P16 M Y 1095.75 40.41593932 247.6495456 19.69024684 161.64 6685.6 13 P16 F Y 292225.08300169 231.6043765 9.022844487 902.53 37571.39 14 P16 F Y 12053.2537.49924765 158.6370595 24.90606549 1.63471.15 15 P16 F Y 14610 76.58209602 278.3837309 41.51010914 152.13 16285.49 16 P16 F Y 3287.25 49.58239171 128.4568603 17.91234645 274.99 41823.21 17 P17 M N 2.333079994 397.4440508 55.20987654 366.37 90011.27 18 P17 F N 4.749435461 222.0839813 73.62489675 271.65 903.89 19 P17 F N 1.749468315 676.8904636 47.7037037 721.19 663.15 20 P17 M N 33.24946503 413.712486 27.42386831 611.64 4195.86 21 P17 F N 15.4162131 346.9913086 30.71604938 302.29 2151.47 22 P17 F N 33.3327405 2598.071161 107.8088094 1800.44 102005.12 23 P17 M N 9.832656179 3296.535581 54.1563786 2642.73 676.78 24 P17 F N 3.749446413 488.2589867 15.29151952 562.88 11619.62 25 P17 M N 9.749380705 159.1536586 23.41690259 132.64 931.14 26 P17 M Y 12053.2550.91548265 173.7764722 18.90280088 52.25 15962.05 27 P17 M Y 3652.5 25.83248096 264.8254141 35.32510288 497.33 15504.95 28 P17 F Y 28.41607073 415.3599225 35.0617284 1600.67 14224.39 29 P17 F Y 6209.25 60.74882219 213.7280879 44.41152263 111.36 9018.48 30 P17 M Y 4748.25 47.33258719 264.0016959 31.24279835 366.81 3809.83 31 P17 M Y 16071 54.49906148 112.4128794 34.40329218 114.56 1727.02 32 P17 M Y 7670.25 52.33253243 145.5753317 32.2962963 44.92 15264.84 33 P17 M Y 876631.74913978 220.2561296 34.40329218 130.31 2377.36 34 P17 F Y 8400.75 40.83231669 194.6662059 48.09876543 407.83 19587.61 35 P17 M Y 12053.2536.1661567 212.1613578 96.51775947 621.42 3269.9 36 P17 M Y 8035.5 57.91540599 115.2852178 24.79012346 282.88 8960.27 37 P17 M Y 5478.75 36.33270765 160.4592669 40.72427984 102.32 5006.77 38 P17 F Y 9496.5 34.74910692 329.8991551 40.32921811 417.32 248857.58 39 P18 F N 14.2496731 538.5430144 54.34303351 396
