parse.gctx() dimnames error

[rpeys]

I am getting an error in parse.gctx() which I can't figure out.
I run parse.gctx("../fpkm_limit_baseline_cd138.gct") and get this error:

parsing as GCT v1.2
../fpkm_limit_baseline_cd138.gct 55861 rows, 770 cols, 0 row descriptors, 0 col descriptors
Error in dimnames(mat) = list(rid, cid) :
length of 'dimnames' [2] not equal to array extent
In addition: Warning messages:
1: In matrix(mat, nrow = nrmat, ncol = ncmat + nrhd + col_offset, byrow = TRUE) :
data length [43068831] is not a sub-multiple or multiple of the number of columns [772]
2: In matrix(as.numeric(mat[, (1 + col_offset):ncol(mat)]), nrow = nrmat, :
NAs introduced by coercion

Any ideas how to get past this? My file is a gct not gctx file. It's extension is .gct, and here is a snapshot of the first few rows/columns:

I am using cmapR version 1.0.1, and here is my session info:

$platform
[1] "x86_64-apple-darwin15.6.0"

$arch
[1] "x86_64"

$os
[1] "darwin15.6.0"

$system
[1] "x86_64, darwin15.6.0"

$status
[1] ""

$major
[1] "3"

$minor
[1] "5.1"

$year
[1] "2018"

$month
[1] "07"

$day
[1] "02"

$svn rev
[1] "74947"

$language
[1] "R"

$version.string
[1] "R version 3.5.1 (2018-07-02)"

$nickname
[1] "Feather Spray"

[tnat1031]

Hi Rebecca, It looks to me like perhaps the gct file you're using doesn't strictly conform to the GCT v1.2 spec, but I can't see anything obviously wrong with it from the screenshot. Is there any chance you could send me or point me to the the file so I could do some testing? Thanks a lot, Ted

…

On Fri, Oct 19, 2018 at 12:49 PM Rebecca Peyser ***@***.***> wrote: I am getting an error in parse.gctx() which I can't figure out. I run parse.gctx("../fpkm_limit_baseline_cd138.gct") and get this error: parsing as GCT v1.2 ../fpkm_limit_baseline_cd138.gct 55861 rows, 770 cols, 0 row descriptors, 0 col descriptors Error in dimnames(mat) = list(rid, cid) : length of 'dimnames' [2] not equal to array extent In addition: Warning messages: 1: In matrix(mat, nrow = nrmat, ncol = ncmat + nrhd + col_offset, byrow = TRUE) : data length [43068831] is not a sub-multiple or multiple of the number of columns [772] 2: In matrix(as.numeric(mat[, (1 + col_offset):ncol(mat)]), nrow = nrmat, : NAs introduced by coercion Any ideas how to get past this? My file is a gct not gctx file. It's extension is .gct, and here is a snapshot of the first few rows/columns: [image: image] <https://user-images.githubusercontent.com/19732554/47190473-9ace9480-d30f-11e8-9bad-45e6aaa79d21.png> I am using cmapR version 1.0.1, and here is my session info: $platform [1] "x86_64-apple-darwin15.6.0" $arch [1] "x86_64" $os [1] "darwin15.6.0" $system [1] "x86_64, darwin15.6.0" $status [1] "" $major [1] "3" $minor [1] "5.1" $year [1] "2018" $month [1] "07" $day [1] "02" $svn rev [1] "74947" $language [1] "R" $version.string [1] "R version 3.5.1 (2018-07-02)" $nickname [1] "Feather Spray" — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#23>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB3i7zUFqpgOdJEki9zksm_J30ucmQhBks5umgKWgaJpZM4Xw-Ru> .

[rpeys]

Thank you, @tnat1031 ! Here is a link to the gct file: https://www.dropbox.com/s/vs8503sziwqb0cq/fpkm_limit_baseline_cd138.gct?dl=0

[tnat1031]

Hi Rebecca, Thanks for pointing me to the file. After taking a closer look, I think there are a couple issues. One is that the number of data columns in the file appears to be 769, but in the header (second row of file) this is indicated as 770. The other is that two of the row ids seem to be duplicated. These row is are "1-Mar" and "2-Mar'. My suspicion is that these are gene symbols that were auto-converted to dates by a program like excel. Do you know if this is how the file was created? Changing the number of columns and de-duplicating the row ids should enable you to parse the file using `parse.gctx`. Can you please let me know if that works for you? Thanks a lot, Ted

…

On Sat, Oct 20, 2018 at 9:31 PM Rebecca Peyser ***@***.***> wrote: Thank you, @tnat1031 <https://github.com/tnat1031> ! Here is a link to the gct file: https://www.dropbox.com/s/vs8503sziwqb0cq/fpkm_limit_baseline_cd138.gct?dl=0 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#23 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AB3i7_aHBif6uz-PYrUnx9JNpiYsoyD7ks5um85wgaJpZM4Xw-Ru> .