Question: Evaluating Differential Expressed Genes from NimbleGen Pair Data using R oligo package
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gravatar for morovatunc
3.8 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

I would like to perform differential expressed Genes analysis of a NimbleGen data. I have dataset of 48 .pair files and 48 .calls files. 

1) Can I perform DE genes analysis only with these data + ndf file without using oligo package? ( my data contains single channel only 532 output) 

2)I have read that oligo packages uses only xys files so i tried to transform my .pair data to xys data using theileria.org's create_xys_files.pl script under AHDW project. We have extracted X Y and Signal values from the .pair files and inserted Count column. In the Count column, we entered NA for missing values. 

After we do this, read.xysfiles() gave us All the XYS files must be of the same type. Error : checkChipTypes(filenames, verbose:'nimblegen') is not TRUE.

So what is the true way of transforming pair data to xys.

Our pair files don't include header line somehow. I have seen that this header line contains some information ? (which starts with # software=NimbleScan)

Please help me 

Thank you in andvace

Best Regards

Tunc

 

 

ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by morovatunc400
0
gravatar for morovatunc
3.8 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

Also want to add : 

our array was NimbleGen Human Gene Expression 12x135K Array [100718_HG18_opt_expr] - GPL18943

 

Thank you in advance

ADD COMMENTlink written 3.8 years ago by morovatunc400
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