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Yongde Bao ▴ 170
@yongde-bao-244
Last seen 10.3 years ago
Hi. Since updating my R and BioC a few days ago, I have been hit with the following warnings 1: the condition has length > 1 and only the first element will be used in: if is.na(ans[[i]])) next 2 . . . 50 It showed up even when I did the demo(affy). Can someone tell me what went wrong? Thanks, Yongde Yongde Bao, Ph.D Biomolecular Research Facility Department of Microbiology University of Virginia School of Medicine Charlottesville, VA 22908 E-mail: yb8d@virginia.edu Voice mail: 434-982-2551, 434-924-2553 FAX: 434-982-2514
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@knud-josefsen-290
Last seen 10.3 years ago
After upgrading to R 1.7 I constantly get this message There were 50 or more warnings (use warnings() to see the first 50) > warnings() Warning messages: 1: the condition has length > 1 and only the first element will be used in: if is.na(ans[[i]])) next 2: ... Some things works, others not. Any suggestions? Thank you! Knud [[alternate HTML version deleted]]
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what function/package does this? in affy this will go away in the next release. you can get the current developmental version to get rid of them now. On Sun, 11 May 2003, Knud Josefsen wrote: > After upgrading to R 1.7 I constantly get this message > > There were 50 or more warnings (use warnings() to see the first 50) > > > warnings() > Warning messages: > 1: the condition has length > 1 and only the first element will be used in: if is.na(ans[[i]])) next > 2: ... > > Some things works, others not. Any suggestions? > > Thank you! > > Knud > [[alternate HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
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rinku saha ▴ 30
@rinku-saha-295
Last seen 10.3 years ago
1)I installed R-1.7.0 in Sgi machine(irix6.5).I installed all the > > bioconductor packages too. > > After that i did put all my >cel files under one directory and then move > > into that directory and Start R.Then i gave library(affy) to load it. > > Welcome to Bioconductor > > To view some introductory material......... > > Simply type....... > > Creating a new generic function for "summary" in package > > Biobase > > {1} TRUE > > > > My question is did it reall yy load the package affy. > > > > 2)When i write data <-ReadAffy() > > it gives these: > > > > 1: the condition has length > 1 and only the first element will be used >in: > > if (dim(intensity(cel)) != dim.intensity) stop(paste("CEL file dimension > > mismatch !\n(file", > > > > My question is how can i make it work to read my .cel file. > > I am sending you an example .cel file > > [CEL] > > Version=3 > > > > [HEADER] > > Cols=536 > > Rows=536 > > TotalX=536 > > TotalY=536 > > OffsetX=0 > > OffsetY=0 > > GridCornerUL=237 234 > > GridCornerUR=4492 243 > > GridCornerLR=4490 4508 > > GridCornerLL=235 4499 > > Axis-invertX=0 > > AxisInvertY=0 > > swapXY=0 > > DatHeader=[73..46225] MG2000062256AA:CLS=4733 RWS=4733 XIN=3 YIN=3 >VE=17 > > 2.0 06/22/ 0 11:15:55 GridVerify=Success Hu6800.1sq > > 6 > > Algorithm=Percentile > > >AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;Outl ierLow:1.004 > > > > [INTENSITY] > > NumberCells=287296 > > CellHeader=X Y MEAN STDV NPIXELS > > 0 0 1447.3 294.2 36 > > 1 0 34282.8 4017.5 36 > > 2 0 1528.0 244.9 36 > > 3 0 33889.3 4679.7 36 > > 4 0 1073.5 211.4 36 > > 5 0 1493.8 235.2 36 > > 6 0 26558.8 5903.9 36 > > 7 0 1557.5 259.3 36 > > 8 0 25951.8 3178.6 30 > > 9 0 1497.0 292.3 36 > > 10 0 26122.8 3989.7 36 > > 11 0 1577.3 271.9 36 > > 12 0 25029.8 4386.5 36 > > 13 0 1454.8 229.0 36 > > 14 0 25128.5 5666.1 36 > > 15 0 1602.0 242.9 36 > > 16 0 26180.0 6859.9 36 > > 17 0 1652.8 304.7 36 > > 18 0 26311.8 7985.2 36 > > 19 0 1655.0 295.9 36 > > 20 > > > > > > > > 3)when i try to load tcl/tk it says: > > Loading required package: tcltk > > Error in firstlib(which.lib.loc, package) : > > Tcl/Tk support is not available on this syError: syntax error > > Please do help me out. > > > > Thanks > > RInku > > > > _________________________________________________________________ > > Mega movies. Mega prizes. >http://server1.msn.co.in/sp03/hallmark/index.asp > > Switch to Hallmark channel. > > > > ______________________________________________ > > R-help@stat.math.ethz.ch mailing list > > https://www.stat.math.ethz.ch/mailman/listinfo/r-help > > > > _________________________________________________________________ Looking for a laptop? Get cool deals. http://www.baazee.com/static/Category152.html?MarketMedId=408 Only on Baazee.
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On Thu, May 15, 2003 at 06:31:07PM +0530, rinku saha wrote: > > > > 1)I installed R-1.7.0 in Sgi machine(irix6.5).I installed all the > >> bioconductor packages too. > >> After that i did put all my >cel files under one directory and then move > >> into that directory and Start R.Then i gave library(affy) to load it. > >> Welcome to Bioconductor > >> To view some introductory material......... > >> Simply type....... > >> Creating a new generic function for "summary" in package > >> Biobase > >> {1} TRUE > >> > >> My question is did it reall yy load the package affy. > >> > >> 2)When i write data <-ReadAffy() > >> it gives these: > >> > >> 1: the condition has length > 1 and only the first element will be used > >in: > >> if (dim(intensity(cel)) != dim.intensity) stop(paste("CEL file dimension > >> mismatch !\n(file", those are 'warnings'. They do not cause harm. Your data were loaded. I would suggest you try the devel version. (note: "data" is an helpful function in R. Try to find an another name for your variable) Hopin' it helps, L. > >> > >> My question is how can i make it work to read my .cel file. > >> I am sending you an example .cel file > >> [CEL] > >> Version=3 > >> > >> [HEADER] > >> Cols=536 > >> Rows=536 > >> TotalX=536 > >> TotalY=536 > >> OffsetX=0 > >> OffsetY=0 > >> GridCornerUL=237 234 > >> GridCornerUR=4492 243 > >> GridCornerLR=4490 4508 > >> GridCornerLL=235 4499 > >> Axis-invertX=0 > >> AxisInvertY=0 > >> swapXY=0 > >> DatHeader=[73..46225] MG2000062256AA:CLS=4733 RWS=4733 XIN=3 YIN=3 > >VE=17 > >> 2.0 06/22/ 0 11:15:55 GridVerify=Success Hu6800.1sq > >> 6 > >> Algorithm=Percentile > >> > >AlgorithmParameters=Percentile:75;CellMargin:2;OutlierHigh:1.500;Ou tlierLow:1.004 > >> > >> [INTENSITY] > >> NumberCells=287296 > >> CellHeader=X Y MEAN STDV NPIXELS > >> 0 0 1447.3 294.2 36 > >> 1 0 34282.8 4017.5 36 > >> 2 0 1528.0 244.9 36 > >> 3 0 33889.3 4679.7 36 > >> 4 0 1073.5 211.4 36 > >> 5 0 1493.8 235.2 36 > >> 6 0 26558.8 5903.9 36 > >> 7 0 1557.5 259.3 36 > >> 8 0 25951.8 3178.6 30 > >> 9 0 1497.0 292.3 36 > >> 10 0 26122.8 3989.7 36 > >> 11 0 1577.3 271.9 36 > >> 12 0 25029.8 4386.5 36 > >> 13 0 1454.8 229.0 36 > >> 14 0 25128.5 5666.1 36 > >> 15 0 1602.0 242.9 36 > >> 16 0 26180.0 6859.9 36 > >> 17 0 1652.8 304.7 36 > >> 18 0 26311.8 7985.2 36 > >> 19 0 1655.0 295.9 36 > >> 20 > >> > >> > >> > >> 3)when i try to load tcl/tk it says: > >> Loading required package: tcltk > >> Error in firstlib(which.lib.loc, package) : > >> Tcl/Tk support is not available on this syError: syntax error > >> Please do help me out. > >> > >> Thanks > >> RInku > >> > >> _________________________________________________________________ > >> Mega movies. Mega prizes. > >http://server1.msn.co.in/sp03/hallmark/index.asp > >> Switch to Hallmark channel. > >> > >> ______________________________________________ > >> R-help@stat.math.ethz.ch mailing list > >> https://www.stat.math.ethz.ch/mailman/listinfo/r-help > >> > > > > > > _________________________________________________________________ > Looking for a laptop? Get cool deals. > http://www.baazee.com/static/Category152.html?MarketMedId=408 Only on > Baazee. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- currently at the National Yang-Ming University in Taipei, Taiwan -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent
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