a problem of package ""
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0
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@3a7d6b0b
Last seen 11 months ago
Hong Kong

i just met a warning below when i tried to run these code:

options(stringsAsFactors = F)
> f='GSE154851_eSet.Rdata'
>
> library(GEOquery)
> #Setting options('GEOquery.inmemory.gpl'=FALSE)
> if(!file.exists(f)){
+     gset <- getGEO('GSE154851', destdir=".",
+                    AnnotGPL = F,
+                    getGPL = F)
+     save(gset,file=f)
+ }


the warning:

Warning: 1 parsing failure.
row col   expected     actual                               file
1672  -- 71 columns 48 columns './GSE154851_series_matrix.txt.gz'


MY question is: what does it mean?(Does it mean that the result is not available for next-step analysis?) How can I solve it?

Sheldon

GEO GEOquery • 442 views
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Hi,

It would be nice if you could edit the title of your post to make it somewhat more meaningful. Not just for aesthetics but to make questions searchable. This helps make the support site a resource that is more useful to the community.

Thanks,

H.

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Basti ▴ 280
@7d45153c
Last seen 1 hour ago
France

If you are trying to download GSE154851 data on your machine, I just performed gset <- getGEO('GSE154851', destdir=".",AnnotGPL = F, getGPL = F) and I didn't get any error message, I think you could do the same

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honestly, I am not a professional user at all, i copied code that they uploaded on the tutorial website. So typically i have no idea about modifying code hhhh. Because there is another data which is invalided on GEO2R, i have to use Rstudio. Thank uuuuu Kevin!

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yes i got what i want through your method! thank you Basti, again!!!!

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I neither see any warning nor error messages when running this code. sheldon19931016, can you please verify?

Note also the helpful code via GEO2R: https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE154851