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Question: Error when using readIDAT() from illuminaio
0
gravatar for lacion
2.8 years ago by
lacion0
Argentina
lacion0 wrote:

Hi All,

I am trying to read an idat file from an Illumina genotyping array that uses VeraCode microbeads technology. This is my code and the error I get:

> library(illuminaio)
> idat <- readIDAT("E:/Ck01EC032-VBP_R001_C001_GRN.idat")
Error in idx[i, 1] : subscript out of bounds

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] IlluminaDataTestFiles_1.3.1 illuminaio_0.8.0           

loaded via a namespace (and not attached):
[1] base64_1.1  tools_3.1.2

Any help is greatly appreciated.

Thank you,

Laura

ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by lacion0
0
gravatar for Kasper Daniel Hansen
2.8 years ago by
United States
Kasper Daniel Hansen6.3k wrote:
Is it possible to make the file available so we can debug this (which may take some time before we get to it, to be honest)? On Thu, Feb 19, 2015 at 3:31 PM, lacion [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User lacion <https: support.bioconductor.org="" u="" 7302=""/> wrote Question: > Error when using readIDAT() from illuminaio > <https: support.bioconductor.org="" p="" 65104=""/>: > > Hi All, > > I am trying to read an idat file from an Illumina genotyping array that > uses VeraCode microbeads technology. This is my code and the error I get: > > > library(illuminaio) > > idat <- readIDAT("E:/Ck01EC032-VBP_R001_C001_GRN.idat") > Error in idx[i, 1] : subscript out of bounds > > > sessionInfo() > R version 3.1.2 (2014-10-31) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] IlluminaDataTestFiles_1.3.1 illuminaio_0.8.0 > > loaded via a namespace (and not attached): > [1] base64_1.1 tools_3.1.2 > > Any help is greatly appreciated. > > Thank you, > > Laura > > ------------------------------ > > You may reply via email or visit Error when using readIDAT() from illuminaio >
ADD COMMENTlink written 2.8 years ago by Kasper Daniel Hansen6.3k
0
gravatar for lacion
2.8 years ago by
lacion0
Argentina
lacion0 wrote:

Thank you for the fast reply, Kasper.

I will be happy to share the file with you. What is the most convenient way to share it?

Laura

ADD COMMENTlink written 2.8 years ago by lacion0
Whatever is easiest for you. If we could pick, on dropbox or on a url somewhere which is not password protected. Kasper On Thu, Feb 19, 2015 at 3:43 PM, lacion [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User lacion <https: support.bioconductor.org="" u="" 7302=""/> wrote Answer: > Error when using readIDAT() from illuminaio > <https: support.bioconductor.org="" p="" 65104="" #65106="">: > > Thank you for the fast reply, Kasper. > > I will be happy to share the file with you. What is the most convenient > way to share it? > > Laura > > ------------------------------ > > You may reply via email or visit > A: Error when using readIDAT() from illuminaio >
ADD REPLYlink written 2.8 years ago by Kasper Daniel Hansen6.3k
0
gravatar for lacion
2.8 years ago by
lacion0
Argentina
lacion0 wrote:

Dropbox it is: https://www.dropbox.com/s/wsls0eb0hkovi3n/Ck01EC032-VBP_R001_C001_GRN.idat?dl=0

Thank you, Kasper!

Laura

________

Laura Acion, PhD

University of Iowa, USA

National Scientific and Technical Research Council, Argentina

lacion@gmail.com

ADD COMMENTlink written 2.8 years ago by lacion0

Hi Laura,

Thanks for posting this.  I've taken a quick look and it looks like the VeraCode idat is encrypted, which is handled with by the part of illuminaio that I'm responsible for.  Until now I've only ever seen expression BeadChip data in this format, so there's probably some assumptions that don't hold for your data.  I'll take a longer look and let you know once it's sorted.

Mike

ADD REPLYlink written 2.7 years ago by Mike Smith2.1k
0
gravatar for Mike Smith
2.7 years ago by
Mike Smith2.1k
EMBL Heidelberg / de.NBI
Mike Smith2.1k wrote:

Hi Laura,

If you check out version 0.9.1 from the Biconductor devel branch illuminaio should now be able to read the file you uploaded.  I've never worked with VeraCode data, so I'm not sure what to expect the output to look like, but there's a lot of 0s and not many intensities.  Perhaps that's what you're expecting, but if it isn't please contact me and we'll work on making sure illuminaio is reading the data correctly.

Thanks,

Mike

ADD COMMENTlink written 2.7 years ago by Mike Smith2.1k
0
gravatar for lacion
2.7 years ago by
lacion0
Argentina
lacion0 wrote:

Hi Mike,

Thanks a lot for looking into this. I was able to open our files using the new version of illuminaio. It seems the file I sent you was problematic and that is why you were getting a lot of 0s. A different file yields:

> head(idat$Quants)
  MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData
1   11774.799         11884.2500  1000.1562    12031.4170                 0
2    5392.514          5422.7046   242.7697     5300.4170                 0
3    2880.954          2891.2720   116.9060     2865.5835                 0
4     135.381           140.1218    63.5149      123.0833                 0
5    3670.702          3690.5874   225.5330     3688.9167                 0
6    3231.911          3263.2666   225.6001     3187.0833                 0
  BackgroundDevBinData CodesBinData NumBeadsBinData NumGoodBeadsBinData
1                    0           10              17                  17
2                    0           23              12                  12
3                    0           33              20                  20
4                    0           44              14                  14
5                    0           51              21                  21
6                    0           54              16                  16

We are new to VeraCode data too, but this is more reassuring than all 0s :-)

Thanks a lot for your help.

Best wishes,

Laura

ADD COMMENTlink written 2.7 years ago by lacion0
Looks great to me. Thanks for fixing this Mike. Should we add a file like this to IlluminaTestDataFiles, assuming Laura is willing to contribute and put it in the open domain? Kasper On Wed, Mar 4, 2015 at 11:08 AM, lacion [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User lacion <https: support.bioconductor.org="" u="" 7302=""/> wrote Answer: > Error when using readIDAT() from illuminaio > <https: support.bioconductor.org="" p="" 65104="" #65374="">: > > Hi Mike, > > Thanks a lot for looking into this. I was able to open our files using the > new version of illuminaio. It seems the file I sent you was problematic and > that is why you were getting a lot of 0s. A different file yields: > > > head(idat$Quants) > MeanBinData TrimmedMeanBinData DevBinData MedianBinData BackgroundBinData > 1 11774.799 11884.2500 1000.1562 12031.4170 0 > 2 5392.514 5422.7046 242.7697 5300.4170 0 > 3 2880.954 2891.2720 116.9060 2865.5835 0 > 4 135.381 140.1218 63.5149 123.0833 0 > 5 3670.702 3690.5874 225.5330 3688.9167 0 > 6 3231.911 3263.2666 225.6001 3187.0833 0 > BackgroundDevBinData CodesBinData NumBeadsBinData NumGoodBeadsBinData > 1 0 10 17 17 > 2 0 23 12 12 > 3 0 33 20 20 > 4 0 44 14 14 > 5 0 51 21 21 > 6 0 54 16 16 > > We are new to VeraCode data too, but this is more reassuring than all 0s > :-) > > Thanks a lot for your help. > > Best wishes, > > Laura > > ------------------------------ > > You may reply via email or visit > A: Error when using readIDAT() from illuminaio >
ADD REPLYlink written 2.7 years ago by Kasper Daniel Hansen6.3k
0
gravatar for lacion
2.7 years ago by
lacion0
Argentina
lacion0 wrote:

Hi Kasper and Mike,

If you decide to add a VeraCode file to IlluminaTestDataFiles you can find the one I included in my previous post here: https://www.dropbox.com/s/vhaah8gu2k7p3sz/TestPlaca1R004_C005_RED.idat?dl=0

Thanks again for fixing this so fast.

Best wishes,

Laura

ADD COMMENTlink written 2.7 years ago by lacion0

That's great, thanks very much.  

ADD REPLYlink written 2.7 years ago by Mike Smith2.1k
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