[R] you are making it far too difficult
Caitlin Gibbons
bioprogr@mmer @ending from gm@il@com
Thu Dec 27 22:30:27 CET 2018
“\t” is an escape sequence which signifies one tab character. “/t” is NOT an escape sequence, and to R, looks like a very brief file path.
Sent from my iPhone
> On Dec 27, 2018, at 2:09 PM, Spencer Brackett <spbrackett20 using saintjosephhs.com> wrote:
>
> What is the significance of using / or \ ?
>
>> On Thu, Dec 27, 2018 at 4:02 PM Sarah Goslee <sarah.goslee using gmail.com> wrote:
>>
>> On Thu, Dec 27, 2018 at 2:03 PM Spencer Brackett
>> <spbrackett20 using saintjosephhs.com> wrote:
>>>
>>> Thank you for the help! I tried using the read.table command in my
>> RStudio
>>> using the following argument, and managed to open the file.
>>>
>>> GBM_protein_expression<-read.table(file.choose(), header=TRUE, sep=“/t”)
>>
>> Note that sep="/t" is NOT the same thing as the sep="\t" you were
>> advised to use.
>>
>>
>>
>>
>>>
>>> However, my data did not unpack as yours did. I again only received a
>> table
>>> of true and flase distinctions per column, and my environment tab says
>> that
>>> there is 0 observations upon 0 variables.
>>>
>>> I believe I should be getting data similar to what you got, as it would
>>> appear that your’s actually contains relevant gene/protein expression
>> info.
>>>
>>> On Thu, Dec 27, 2018 at 6:21 AM Federico Calboli <
>>> federico.calboli using kuleuven.be> wrote:
>>>
>>>> Once you have your TSV files just use something as
>>>>
>>>> x = read.table('protein_expression.tsv', h = T, sep = '\t')
>>>>
>>>> Do not copy paste the code of this email because it is formatted and
>> would
>>>> not work in R.
>>>>
>>>>
>>>> Best
>>>>
>>>> F
>>>>
>>>> PS the data looks like this to me
>>>>
>>>> head(x)
>>>> icgc_donor_id project_code icgc_specimen_id icgc_sample_id
>>>> submitted_sample_id analysis_id antibody_id gene_name
>>>> 1 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 14-3-3_epsilon-M-C YWHAE
>>>> 2 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 4E-BP1-R-V EIF4EBP1
>>>> 3 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 4E-BP1_pS65-R-V EIF4EBP1
>>>> 4 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 4E-BP1_pT37-R-V EIF4EBP1
>>>> 5 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 4E-BP1_pT70-R-C EIF4EBP1
>>>> 6 DO12370 GBM-US SP26475 SA131594
>>>> TCGA-19-5960-01A-13-1900-20 97765 53BP1-R-C TP53BP1
>>>> gene_stable_id gene_build_version normalized_expression_level
>>>> verification_status verification_platform
>>>> 1 NA NA -1.1636330
>>>> not tested NA
>>>> 2 NA NA -1.7969721
>>>> not tested NA
>>>> 3 NA NA -0.7256390
>>>> not tested NA
>>>> 4 NA NA 0.6498421
>>>> not tested NA
>>>> 5 NA NA -1.0262844
>>>> not tested NA
>>>> 6 NA NA 1.5186400
>>>> not tested NA
>>>> platform
>>>> 1 M.D. Anderson Reverse Phase Protein Array Core
>>>> 2 M.D. Anderson Reverse Phase Protein Array Core
>>>> 3 M.D. Anderson Reverse Phase Protein Array Core
>>>> 4 M.D. Anderson Reverse Phase Protein Array Core
>>>> 5 M.D. Anderson Reverse Phase Protein Array Core
>>>> 6 M.D. Anderson Reverse Phase Protein Array Core
>>>>
>>>>
>>>>
>>>> experimental_protocol
>>>> 1 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 2 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 3 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 4 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 5 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> 6 MDA_RPPA_Core
>>>>
>> http://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/blca/cgcc/mdanderson.org/mda_rppa_core/protein_exp/mdanderson.org_BLCA.MDA_RPPA_Core.mage-tab.1.7.0/mdanderson.org_BLCA.MDA_RPPA_Core.idf.txt
>>>> raw_data_repository raw_data_accession
>>>> 1 TCGA TCGA-19-5960-01A-13-1900-20
>>>> 2 TCGA TCGA-19-5960-01A-13-1900-20
>>>> 3 TCGA TCGA-19-5960-01A-13-1900-20
>>>> 4 TCGA TCGA-19-5960-01A-13-1900-20
>>>> 5 TCGA TCGA-19-5960-01A-13-1900-20
>>>> 6 TCGA TCGA-19-5960-01A-13-1900-20
>>>>
>>
>>
>> --
>> Sarah Goslee (she/her)
>> http://www.numberwright.com
>>
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
More information about the R-help
mailing list