Video for downloading the data

Hi everyone!

I recorded a video of how to download the data from GEO in case anyone has any trouble. Good luck with the deliverables!
https://drive.google.com/file/d/1Bwt39g0UqJ8Ws1SfGKf72RKFysUfVMvH/view?usp=sharing

1 Like

Hi!
Thank you for making the video-it was very helpful!

I followed the instructions, but when I upload everything in RStudio, it says that the object is not found. I have named one set transcriptome1, and when I run the code, it says ‘transcriptome1’ not found.

Thank you!

So after unzipping everything, when you put it in the data folder in the R directory, and try to read it, it says that it can’t be found?
I’m not sure why that could be, if you put the celfile.path right, I believe it should work:-? I don’t know if this will work but it might help just deleting it and try to put it again in the folder and read it again?

Thanks for making the video Anca, it’s very clear and concise!

I wonder if you may be able to help me… as I’ve been having an importing issue with my data onto Rstudio for a while. I’m having a similar issue to Ena_Haseljic.

In the video you right click and unzip the folder. But when I right click I can’t unzip anything. I also didn’t know that that was a step we had to do.

But I already have the data under the “files” tab on Rstudio. But I haven’t done the unzipping step.
I write in upper left hand corner box:
dataset17 <- ReadAffy(celfile.path = “data_pipeline/GSE32323_RAW(3).tar”)
dataset32 <- ReadAffy(celfile.path = “data_pipeline/GSE8671_RAW.tar”)

but in the consol it says this:

dataset17 <- ReadAffy(celfile.path = “data_pipeline/GSE32323_RAW(3).tar”)
Error in AllButCelsForReadAffy(…, filenames = filenames, widget = widget, :
No cel filennames specified and no cel files in specified directory:data_pipeline/GSE32323_RAW(3).tar

dataset32 <- ReadAffy(celfile.path = “data_pipeline/GSE8671_RAW.tar”)
Error in AllButCelsForReadAffy(…, filenames = filenames, widget = widget, :
No cel filennames specified and no cel files in specified directory:data_pipeline/GSE8671_RAW.tar

I was thinking that maybe it’s because either I didn’t unzip the file or because for some reason either I or Rstudio are confused on where the directory is.

Please let me know your thoughts,
Olivia

Hi @Sail19!

What laptop do you have? The unzipping step is very important because the ReadAffy function can’t just read through the tar file type. It works just with cel files so they need to be unzipped.
If you have a mac, I believe it might work if you just double click on the file and then it should create the folder and unzip the file. If that doesn’t work, when you right click you should see either an option that contains unzip, or something like Extract to. Please let me know if this still doesn’t work!
I am just tagging @yvesgaetan who might have other suggestions too, because he has more experience than me.

Oh no worries, derburg7 helped me out. So it’s all good. I just didn’t know that I was supposed to download another thing for a windows computer.

oh great, I’m glad you figured it out!

Hey!

I am still having the same problem and the same message appears. Would you be able to tell me what you had to download for Windows?
Thank you!

Hi, I fixed the problem! Thanks