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• 1

  Matthías Macé

  04 August 2009 | 07:25

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  Hi Vineeta
  What do you want to do exactly with genotyping data: association, linkage, … ? Or do you only want to process the signal (e.g. from micro-arrays ) ?
  Morover, you should precise the kind of genotyping data (from micro-arrays, sequencing, …).
  PLease feel free to send a message for further information.
  Matthias

• 2

  vineeta singh

  05 August 2009 | 05:14

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  Hi Matthias

  first of all thanx for reply.I am very new into genotyping data analysis have idea from where to start and end. My company work on Illumina platform for genotyping and gene expression exp. we do whole genome genotyping based on 660K SNP chip.Illumina provides with Genome Studio software for preliminary analysis like quality check,data curation,Intensity normalization.
  I want to proceed further into advanced analysis for GWAS using computational softwares( expecially pLink or R Bioconductor).Regarding my statistics and computational knowledge am well acquaint with basics.
  Kindly help and guide me how to Proceed with this aim.

• 3

  vineeta singh

  05 August 2009 | 05:26

  [ Permalink ]

  Hi Matthias

  first of all thanx for reply.I am very new into genotyping data analysis have no idea from where to start and end. My company work on Illumina platform for genotyping and gene expression exp. we do whole genome genotyping based on 660K SNP chip.Illumina provides with Genome Studio software for preliminary analysis like quality check,data curation,Intensity normalization.
  I want to proceed further into advanced analysis for GWAS using computational softwares( expecially pLink or R Bioconductor).Regarding my statistics and computational knowledge am well acquaint with basics.
  Kindly help and guide me how to Proceed with this aim.

• 4

  atul srivastav

  06 August 2009 | 04:25

  [ Permalink ]

  hi vineeta,

  there are some R packej are avalilable for genotyping data analysis.
  and you can find some software in http://seqanswers.com/forums/index.php

  also its very gud site it all about NGS it will help you a lot.

  Best regards,

  ATuL Srivastav

• 5

  vineeta singh

  07 August 2009 | 05:38

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  I brwosed the URL u given but in this site they hardy giving any infor on software pakages for Illumina genotyping data analysis. In given URL mostly populated with sequncing related information.
  I am very new to this field dont have any idea from where to proceeed. let me know few of the R pakages from which I can start.

• 6

  atul srivastav

  10 August 2009 | 06:35

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  Hi vineeta,

  There is a package named beadarray in R which does the Illumina Genotyping Analysis. Much more you can even use limmaGUI which is a graphical package in R. and illumina it self procived a software for data analysis.
  http://www.illumina.com/pages.ilmn?ID=169

  Best Regards,

  ATul.

• 7

  atul srivastav

  12 August 2009 | 11:28

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  Hi, vineeta,

  did u get those R packejes.?
  where is Amity in HYD.?

• 8

  vineeta singh

  13 August 2009 | 05:03

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  Ya got those R packages I have used Limma for gene expression analysis. U have any idea for pLink software am using Cygwin as linux platform but my commands are not parsing. Is compiler is needed to install???

  Rest Amity,Hyderabad in jubilee hills. Hey you know Pardhu(CCMB) ?
• 9

  atul srivastav

  14 August 2009 | 04:33

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  Hi,
  no i dont have any idea about pLink software, ill check it and let you know.
  ya i know him pardhu he was in Animal lab but now he is working for SANDOR company in banjara hulls is it..? thin guy.

  so in AMity you people are doing research also its know as teaching institute for student..?, i think these things we should not disscus in this group.reply on my this ih.atul.s@ocimumbio.com.

• 10

  atul srivastav

  14 August 2009 | 04:44

  [ Permalink ]

  atul.s@ocimumbio.com

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