How do I create input files required by iGEAK (or find alternatives to iGEAK) for array analysis.

Question

[Bhanu]

I want to perform differential expression on GSE90603_RAW.tar and use the following web-based tool (https://sites.google.com/view/igeak/input-format?authuser=0). I do not understand how I'm supposed to make a "Group-Definition File" and "Gene Expression Matrix" mentioned as the input files. If there is another alternative for this tool (preferably web-based) I'd gladly use it.

Answer 1

[i.sudbery]

Alternatives to iGEAK

You can try GEO2R from the GEO website itself. There is a big blue button towards the end of the GEO record. There are good instructions linked at the top of the resulting page, and even a youtube video.

iGEAK

I've never come across iGEAK before, but the instructions you link do a pretty good job of describing the content of each of the required files.

Annotation file

The annotation file can be obtained from NCBI. You need to select the platform link on the GSE90603 page, and then select "download full table".

Expression Matrix

For the expression matrix, the page suggests using http://arrayanalysis.org to convert the CEL files into an expression matrix. The CEL files are _inside_ GSE90603_RAW.tar, you need to use a program capable of extracting them from the tar file if you want to do that. Something like 7zip on windows. However, the already processed matrix file is available on NCBI.

The file is zipped, and you'll need to unzip it before use. Again, 7zip should be able to do this on windows. You might also need to remove any lines starting with ! from the beginning of the file. You should be able to do this with either Excel, or with notepad.

Condition File

The condition file you will need to make yourself. Either with notepad or excel (remember to save as a "txt (tab-delimited)" file, not an xls/xlsx file). The expriment contains several arrays. You need to tell iGEAK which arrays are cancer, and which are normal. Each array has an ID that starts "GSM", some of them are normal, some are cancer. Which is which is listed in the "samples" section of the GEO record. You'll need to click the "more" button to see them all. Create a file that has in the first column the name of the array (e.g. GSM2407549). In the second column mark whether this is a cancer or normal sample. Do that for all the arrays you want to use as normals and all the arrays you want to use as cancer.

[Bhanu]

Thanks a lot I did actually already use the GEO2R tool but I thought I should look for alternatives but this has helped me a lot.