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Olga Botvinnik
@olgabot
As in, the data frame.loc of the gene
thewilmergency
@thewilmergency
oh ok
Screenshot 2016-02-14 17.34.15.png
It's just slightly different...
I get the same issue when I made my tpm column...
Screenshot 2016-02-14 17.36.26.png
thewilmergency
@thewilmergency
But when I made the log2_tpm column it was okay...
LElmen
@LElmen
Hi, I can't find the info on what to do when login to tscc prompts a password. Anyone?
ericsan119
@ericsan119
@olgabot Hi Olga, for the exercise 13, I think it's correct, but my output is slightly different with yours... Could you give me a hint where I did mistake?
Screen Shot 2016-02-15 at 2.10.55 AM.png
ecpierce
@ecpierce
@LElmen try opening a new terminal window, entering this: ssh-add ~/.ssh/biom262_rsa and then try logging in to tscc again
LElmen
@LElmen
@ecpierce Worked like a charm! Thank you
Pedro Torres
@pjtorres
Hey Olga,

I have been having a similar error to

thewilmergency. I'm on exercise 6 and I'm having before Everything was working the other day and I tried running sns.distplot(s10_featurecounts['/home/ucsd-train20/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam']) and it wont read my file even though it is in my folder.

Pedro Torres
@pjtorres
Figured it out, my output file was going to the wrong place.
vwfu
@vwfu

@olgabot I am getting the following error message in exercise 16 when i try to split the GENCODE IDs: ---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)

<ipython-input-311-1af4887c03b8> in <module>()
11
12
---> 13 featurecounts_s13_specific_genes_ensembl.head()

AttributeError: 'numpy.ndarray' object has no attribute 'head'

@ericsan119 did you add one to the TPM before logging it?
@pjtorres that sounds like you may not have created the variable s10_featurecounts yet
even though the file /home/ucsd-train20/projects/shalek2013/processed_data/S10.Aligned.out.sorted.bam exists, that’s not what that command is doing
that command is looking for a variable called s10_featurecounts
oh you figured it out got it..
@vwfu can you show the full code that’s producing the error?
vwfu
@vwfu

@olgabot featurecounts_s10_specific_genes = featurecounts_s10_specific_genes.copy()
featurecounts_s13_specific_genes = featurecounts_s13_specific_genes.copy()

featurecounts_s10_specific_genes.index.map(lambda x: x.split('.')0)
featurecounts_s13_specific_genes.index.map(lambda x: x.split('.')0)

featurecounts_s10_specific_genes_ensembl = featurecounts_s10_specific_genes.index.map(lambda x: x.split('.')0)
featurecounts_s13_specific_genes_ensembl = featurecounts_s13_specific_genes.index.map(lambda x: x.split('.')0)

featurecounts_s13_specific_genes_ensembl.head()

Olga Botvinnik
@olgabot
You need to add the pd.Series() code around it
Only DataFrames and Series can do.head()
I believe earlier it says to do:
pd.Series(featurecounts_s13_specific_genes.index.map(lambda x: x.split(‘.')[0]))
ack
ugh it formatted the quotes
those are supposed to be quotes
ericsan119
@ericsan119
@olgabot Yes I did...
Screen Shot 2016-02-15 at 3.00.51 PM.png
Olga Botvinnik
@olgabot
@ericsan119 was your TPM calculation correct?
did you have errors there?
someone ran into a problem where their TPM calculation was off in the 12th significant figure or something
Olga Botvinnik
@olgabot
if you’re getting errors that far into the value, don’t worry about it - I will acount for it
ericsan119
@ericsan119
@olgabot I check my calculation again, I didn't errors in exercise 8. So I think my TPM calculation is correct.
Olga Botvinnik
@olgabot
hmm the only thing I can think of is if you ddin’t add one
ericsan119
@ericsan119
Screen Shot 2016-02-15 at 3.24.19 PM.png
Olga Botvinnik
@olgabot
Yeah I’m checking with my answer now
Yeah what you have is correct - since the difference is in the .000000001 range I’ll adjust to ignore it
ericsan119
@ericsan119
Thank you @olgabot
thewilmergency
@thewilmergency
Hi I don't think my S13_featurecounts file is right because my exercise 13 output table doesn't have the row mentioned in the assertion cell
Screenshot 2016-02-15 18.07.34.png
I'm trying to figure out where in the process I didn't get the right file. Here are my S13-relevant files
Screenshot 2016-02-15 18.09.28.png
thewilmergency
@thewilmergency
Actually I might be okay.
Olga Botvinnik
@olgabot
Was it a gtf issue?